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@@ -1,49 +1,251 @@
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<?php
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-// $Id:
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-//
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-// Copyright 2009 Clemson University
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-//
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function tripal_analysis_unigene_init(){
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// Add style sheet
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- drupal_add_css(drupal_get_path('theme', 'tripal').
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- '/css/tripal_analysis_unigene.css');
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+ drupal_add_css(drupal_get_path('theme', 'tripal').'/css/tripal_analysis_unigene.css');
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+}
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+/**
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+*
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+*/
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+function tripal_analysis_unigene_node_info() {
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+ $nodes = array();
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+ $nodes['chado_analysis_unigene'] = array(
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+ 'name' => t('Analysis: Unigene'),
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+ 'module' => 'chado_analysis_unigene',
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+ 'description' => t('A unigene assembly constructed from transcriptomic reads.'),
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+ 'has_title' => FALSE,
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+ 'title_label' => t('Analysis: Unigene'),
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+ 'has_body' => FALSE,
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+ 'body_label' => t('Unigene Analysis Description'),
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+ 'locked' => TRUE
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+ );
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+ return $nodes;
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}
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-
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/*******************************************************************************
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- * HOOK: Implemntation of hook_menu() to provide a call back for EST Assembly Tab
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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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-function tripal_analysis_unigene_menu() {
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- $items['node/%/assembly'] = array(
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- 'title' => t('EST Assemblies'),
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- 'page callback' => 'tripal_analysis_unigene_organism_assembly',
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- 'page arguments' => array(1),
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- 'access callback' => 'tripal_analysis_unigene_node_has_menu',
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- 'access arguments' => array('access chado_analysis content',1),
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- 'type' => MENU_LOCAL_TASK | MENU_NORMAL_ITEM
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+function chado_analysis_unigene_perm(){
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+ return array(
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+ 'access chado_analysis_unigene content',
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+ 'create chado_analysis_unigene content',
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+ 'delete chado_analysis_unigene content',
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+ 'edit chado_analysis_unigene content',
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);
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- return $items;
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}
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+
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/*******************************************************************************
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- * Dynamic addition/removal of menu item
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+ * The following function proves access control for users trying to
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+ * perform actions on data managed by this module
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*/
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-function tripal_analysis_unigene_node_has_menu($type,$vid){
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- // check to see if this node is an organism node
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- $sql = 'SELECT organism_id FROM {chado_organism} WHERE vid = %d';
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- $result = db_query($sql, $vid);
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-
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- // menu status
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- $box_status =variable_get("tripal_analysis_unigene-box-assembly","menu_off");
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-
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- // if this node is not an organism or a feature node then return false
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- // we don't want the menu item to be shown, otherwise get the normal perms
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- if($org_id = db_fetch_object($result)){
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- if(strcmp($box_status,"menu_on")==0){
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- return user_access($type);
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+function chado_analysis_unigene_access($op, $node, $account){
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+ if ($op == 'create') {
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+ return user_access('create chado_analysis_unigene content', $account);
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+ }
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+
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+ if ($op == 'update') {
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+ if (user_access('edit chado_analysis_unigene content', $account)) {
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+ return TRUE;
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+ }
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+ }
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+ if ($op == 'delete') {
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+ if (user_access('delete chado_analysis_unigene content', $account)) {
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+ return TRUE;
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}
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+ }
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+ if ($op == 'view') {
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+ if (user_access('access chado_analysis_unigene content', $account)) {
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+ return TRUE;
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+ }
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+ }
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+ return FALSE;
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+}
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+/**
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+*
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+*/
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+function chado_analysis_unigene_form ($node){
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+
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+ $form = array();
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+
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+ $unigene = $node->analysis->tripal_analysis_unigene;
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+ $unigene_name = $unigene->unigene_name;
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+ $num_reads = $unigene->num_reads;
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+ $num_clusters = $unigene->num_clusters;
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+ $num_contigs = $unigene->num_contigs;
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+ $num_singlets = $unigene->num_singlets;
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+
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+ $form['unigene_name'] = array(
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+ '#title' => t('Unigene Name'),
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+ '#type' => 'textfield',
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+ '#required' => TRUE,
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+ '#description' => t('A distinct name used to identify this unigene'),
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+ '#default_value' => $unigene_name,
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+ );
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+
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+ $form['num_reads'] = array(
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+ '#title' => t('Number of Reads'),
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+ '#type' => 'textfield',
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+ '#required' => FALSE,
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+ '#description' => t('Provide the number of reads, after filtering that were used for input into the assembly'),
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+ '#default_value' => $num_reads,
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+ );
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+
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+ $form['num_clusters'] = array(
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+ '#title' => t('Number of Clusters'),
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+ '#type' => 'textfield',
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+ '#required' => FALSE,
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+ '#description' => t('Provide the number of clusters generated by the asssembly if a clustering mechanism was used for unigene constructions'),
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+ '#default_value' => $num_clusters,
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+ );
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+
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+ $form['num_contigs'] = array(
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+ '#title' => t('Number of Contigs'),
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+ '#type' => 'textfield',
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+ '#required' => FALSE,
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+ '#description' => t('Provide the number of contigs generated by the assembly'),
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+ '#default_value' => $num_contigs,
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+ );
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+
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+ $form['num_singlets'] = array(
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+ '#title' => t('Number of Singlets'),
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+ '#type' => 'textfield',
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+ '#required' => FALSE,
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+ '#description' => t('Provide the number of singlets remaining in the assembly'),
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+ '#default_value' => $num_singlets,
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+ );
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+
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+
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+
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+ // add in the analysis fields
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+ $analysis_form_elements = chado_analysis_form($node);
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+ foreach ($analysis_form_elements as $key => $element){
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+ $form[$key] = $element;
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+ }
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+ return $form;
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+}
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+/**
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+*
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+*/
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+function chado_analysis_unigene_insert($node){
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+ // insert the analysis
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+ chado_analysis_insert($node);
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+
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+ // add the unigene name as a property of the anslysis
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+ tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_name',$node->unigene_name);
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+ tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs);
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+ tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_reads',$node->num_reads);
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+ tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters);
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+ tripal_analysis_insert_property($node->analysis->analysis_id,'analysis_unigene_num_singlets',$node->num_clusters);
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+}
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+/**
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+*
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+*/
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+function chado_analysis_unigene_update($node){
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+ chado_analysis_update($node);
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+
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+ // check to see if the property exists first if not then insert, if it does then update
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+ $unigene_name = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_name');
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+ $num_contigs = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_num_contigs');
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+ $num_reads = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_num_reads');
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+ $num_clusters = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_num_clusters');
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+ $num_singlets = tripal_analysis_get_property($node->analysis_id,'analysis_unigene_num_singlets');
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+
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+
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+ // update the unigene name as a property of the anslysis, but if for some
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+ // reason it's missing then add it (do the same for all properties)
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+ if(count($unigene_name)==0){
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name);
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+ } else {
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+ tripal_analysis_update_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name);
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+ }
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+
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+ if(count($num_contigs)==0){
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs);
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+ } else {
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+ tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_contigs',$node->num_contigs);
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+ }
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+
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+ if(count($num_reads)==0){
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_num_reads',$node->num_reads);
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} else {
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- return FALSE;
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+ tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_reads',$node->num_reads);
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+ }
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+
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+ if(count($num_clusters)==0){
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters);
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+ } else {
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+ tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_clusters',$node->num_clusters);
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+ }
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+
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+ if(count($num_singlets)==0){
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_unigene_num_singlets',$node->num_singlets);
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+ } else {
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+ tripal_analysis_update_property($node->analysis_id,'analysis_unigene_num_singlets',$node->num_singlets);
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+ }
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+
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+
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+}
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+/**
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+*
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+*/
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+function chado_analysis_unigene_delete($node){
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+ // delete the unigene name as a property of the anslysis
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+// tripal_analysis_delete_property($node->analysis_id,'analysis_unigene_name',$node->unigene_name);
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+
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+ chado_analysis_delete($node);
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+}
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+/**
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+*
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+*/
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+function chado_analysis_unigene_view ($node, $teaser = FALSE, $page = FALSE) {
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+ // use drupal's default node view:
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+ $node = node_prepare($node, $teaser);
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+ return $node;
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+}
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+/**
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+*
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+*/
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+function chado_analysis_unigene_load($node){
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+
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+ // load the default set of analysis fields
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+ $additions = chado_analysis_load($node);
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+
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+ // create some variables for easier lookup
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+ $analysis = $additions->analysis;
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+ $analysis_id = $analysis->analysis_id;
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+
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+ // add in the properties
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+ $unigene_name = tripal_analysis_get_property($analysis_id,'analysis_unigene_name');
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+ $num_contigs = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_contigs');
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+ $num_reads = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_reads');
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+ $num_clusters = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_clusters');
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+ $num_singlets = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_singlets');
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+
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+ $analysis->tripal_analysis_unigene->unigene_name = $unigene_name[0]->value;
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+ $analysis->tripal_analysis_unigene->num_contigs = $num_contigs[0]->value;
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+ $analysis->tripal_analysis_unigene->num_reads = $num_reads[0]->value;
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+ $analysis->tripal_analysis_unigene->num_clusters = $num_clusters[0]->value;
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+ $analysis->tripal_analysis_unigene->num_singlets = $num_singlets[0]->value;
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+
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+ // add in organism information using the materialized view
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+ $sql = "SELECT * FROM {organism_unigene_mview} OUM ".
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+ " INNER JOIN {organism} O on OUM.organism_id = O.organism_id ".
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+ "WHERE OUM.analysis_id = %d ".
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+ "ORDER BY O.genus, O.species";
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+ $previous_db = tripal_db_set_active('chado'); // use chado database
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+ $organisms = db_query($sql,$analysis_id);
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+ tripal_db_set_active($previous_db); // now use drupal database
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+
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+ while($organism = db_fetch_object($organisms)){
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+ $sql = "SELECT nid FROM {chado_organism} WHERE organism_id = %d";
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+ $c_org = db_fetch_object(db_query($sql,$organism->organism_id));
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+ $organism->nid = $c_org->nid;
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+ $analysis->tripal_analysis_unigene->organisms[] = $organism;
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}
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+
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+
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+ return $additions;
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}
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/*******************************************************************************
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* tripal_analysis_unigene_nodeapi()
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@@ -59,16 +261,11 @@ function tripal_analysis_unigene_nodeapi(&$node, $op, $teaser, $page) {
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array('chado_feature','chado_organism'));
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// Abort if this node is not one of the types we should show.
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- if (!in_array($node->type, $types_to_show, TRUE)) {
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- // Turn the menu off if it's on
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- $box_status = variable_get("tripal_analysis_unigene-box-assembly","menu_off");
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- if (strcmp($box_status,"menu_on")==0 && $node->type =='chado_organism'){
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- variable_set("tripal_analysis_unigene-box-assembly","menu_off");
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+ if (in_array($node->type, $types_to_show, TRUE)) {
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+ // Add unigene to the content item if it's not a teaser
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+ if ($teaser) {
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+ return '';
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}
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- break;
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- }
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- // Add unigene to the content item if it's not a teaser
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- if (!$teaser) {
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// add the alignment to the feature search indexing
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if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
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@@ -84,14 +281,14 @@ function tripal_analysis_unigene_nodeapi(&$node, $op, $teaser, $page) {
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} else {
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if(strcmp($node->type,'chado_organism')==0){
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- // Show unigene content if not at teaser view
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- $node->content['tripal_analysis_unigene_node_add'] = array(
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- '#value' => theme('tripal_analysis_unigene_node_add', $node),
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+ $node->content['tripal_organism_unigenes'] = array(
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+ '#value' => theme('tripal_organism_unigenes', $node),
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'#weight' => 4
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);
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}
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}
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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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@@ -107,11 +304,25 @@ function tripal_analysis_unigene_theme () {
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'tripal_analysis_unigene_search_result' => array (
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'arguments' => array('node'),
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),
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- 'tripal_analysis_unigene_node_add' => array (
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- 'arguments' => array('node'),
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+ 'tripal_organism_unigenes' => array (
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+ 'arguments' => array('node'=> null),
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+ 'template' => 'tripal_organism_unigenes',
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+ ),
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+ 'tripal_analysis_unigene_base' => array (
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+ 'arguments' => array('node'=> null),
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+ 'template' => 'tripal_analysis_unigene_base',
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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_unigene_preprocess_tripal_organism_unigenes(&$variables){
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+ $node = $variables['node'];
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+ $organism = $node->organism;
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+ $unigenes = tripal_analysis_unigene_load_organism_unigenes($organism);
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+ $node->organism->tripal_analysis_unigene->unigenes = $unigenes;
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+}
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/************************************************************************
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* This function is an extension of the chado_feature_view by providing
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* the markup for the feature object THAT WILL BE INDEXED.
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@@ -431,192 +642,43 @@ function tripal_analysis_unigene_get_alignments($map) {
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}
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/************************************************************************
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*
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-*/
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-function tripal_analysis_unigene_organism_assembly($node){
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- $node = node_load($node);
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- return tripal_analysis_unigene_organism_add($node);
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-}
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-/************************************************************************
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-*
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-*/
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-function theme_tripal_analysis_unigene_node_add ($node){
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-
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- if(strcmp($node->type,'chado_organism')==0){
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- $box_status = variable_get("tripal_analysis_unigene-box-assembly","menu_off");
|
|
|
- if (strcmp($box_status,"menu_off")==0){
|
|
|
- $content = tripal_analysis_unigene_organism_add($node);
|
|
|
- }
|
|
|
- }
|
|
|
- return $content;
|
|
|
-}
|
|
|
-/************************************************************************
|
|
|
-*
|
|
|
*/
|
|
|
-function tripal_analysis_unigene_organism_add($node){
|
|
|
- // get the organism_id for this node:
|
|
|
- $sql = 'SELECT * FROM {chado_organism} WHERE vid = %d';
|
|
|
- $org_id = db_fetch_object(db_query($sql, $node->nid));
|
|
|
-
|
|
|
- // get information about this organism
|
|
|
- $sql = "SELECT * FROM {organism} ".
|
|
|
- "WHERE organism_id = %d";
|
|
|
- $previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
- $organism = db_fetch_object(db_query($sql,$org_id->organism_id));
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|
|
- tripal_db_set_active($previous_db); // now use drupal database
|
|
|
-
|
|
|
- // get information about this assembly and add it to the items in this node
|
|
|
- $sql = "SELECT * FROM {unigene_mview} ".
|
|
|
- "WHERE organism_id = %d ".
|
|
|
- "ORDER BY analysis_id DESC";
|
|
|
+function tripal_analysis_unigene_load_organism_unigenes($organism){
|
|
|
|
|
|
+ // get information about this assemblies and add it to the items in this node
|
|
|
+ $sql = "SELECT * FROM {organism_unigene_mview} OUM ".
|
|
|
+ " INNER JOIN {analysis} A ON A.analysis_id = OUM.analysis_id ".
|
|
|
+ "WHERE OUM.organism_id = %d ".
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|
|
+ "ORDER BY A.timeexecuted DESC";
|
|
|
$previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
- $results = db_query($sql,$org_id->organism_id);
|
|
|
+ $results = db_query($sql,$organism->organism_id);
|
|
|
tripal_db_set_active($previous_db); // now use drupal database
|
|
|
|
|
|
- //$i = 0;
|
|
|
- //while ($assembly = db_fetch_object($results)){
|
|
|
- // get information about this organism and add it to the items in this node
|
|
|
- //$libraries = array();
|
|
|
- //$libraries_sql = "SELECT library_id, library_name ".
|
|
|
- //"FROM {unigene_libraries_mview} ".
|
|
|
- //"WHERE analysis_id = %d ";
|
|
|
- //$previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
- //$libraries_result = db_query($libraries_sql,$assembly->analysis_id);
|
|
|
- //tripal_db_set_active($previous_db); // now use drupal database
|
|
|
- //$library_sql = "SELECT * FROM {chado_library} WHERE library_id = %d";
|
|
|
- //$k = 0;
|
|
|
- //while ($library = db_fetch_object($libraries_result)){
|
|
|
- //$library_node = db_fetch_object(db_query($library_sql,$library->library_id));
|
|
|
- //$library->node_id = $library_node->nid;
|
|
|
- //$libraries[$k++] = $library;
|
|
|
- //}
|
|
|
- //$assembly->libraries = $libraries;
|
|
|
- //$assemblies[$i++] = $assembly;
|
|
|
- //}
|
|
|
-
|
|
|
- // if this content is intended to be a menu item the
|
|
|
- // we need to know so we can format the content slightly different
|
|
|
- $box_status =variable_get("tripal_analysis_unigene-box-assembly","menu_off");
|
|
|
-
|
|
|
- if(count($assemblies) > 0){
|
|
|
- $content = "<div id=\"organism_tab_content\">".
|
|
|
- "<p>New assemblies are built after a significant number of sequences are added to the project or new software is available. ".
|
|
|
- "Click on name for more information.</p><br>";
|
|
|
-
|
|
|
- foreach($assemblies as $assembly){
|
|
|
- $content .= "<div class=\"tripal_unigene-info-box\">".
|
|
|
- "<div class=\"tripal_expandableBox\"><h3><a name=\"$assembly->name\">$assembly->name</a></h3></div>".
|
|
|
- "<div class=\"tripal_expandableBoxContent\">";
|
|
|
- $content .= "<table>".
|
|
|
- "<tr><td class=\"dbfieldname\"> Version </td>".
|
|
|
- " <td class=\"dbfieldvalue\">$assembly->uversion </td></tr>".
|
|
|
- "<tr><td class=\"dbfieldname\"> Analysis ID </td>".
|
|
|
- " <td class=\"dbfieldvalue\">$assembly->analysis_id </td></tr>".
|
|
|
- "<tr><td class=\"dbfieldname\"> Date </td>".
|
|
|
- " <td class=\"dbfieldvalue\">$assembly->adate </td></tr>".
|
|
|
- "<tr><td class=\"dbfieldname\"> Software </td>".
|
|
|
- " <td class=\"dbfieldvalue\">$assembly->program </td></tr>".
|
|
|
- "<tr><td class=\"dbfieldname\"> Software Version </td>".
|
|
|
- " <td class=\"dbfieldvalue\">$assembly->programversion </td></tr>".
|
|
|
- "<tr><td class=\"dbfieldname\"> Number of Contigs </td>".
|
|
|
- " <td class=\"dbfieldvalue\">$assembly->num_contigs </td></tr>".
|
|
|
- "<tr><td class=\"dbfieldname\"> Description </td>".
|
|
|
- " <td class=\"dbfieldvalue\">$assembly->description </td></tr>".
|
|
|
- "<tr><td class=\"dbfieldname\"> Libraries Included in Assembly </td>".
|
|
|
- " <td class=\"dbfieldvalue\"> ";
|
|
|
-//# TODO: THIS SHOULD NOT HAVE A LINK IF THERE IS NO LIBRARY NODE IN DRUPAL
|
|
|
- //foreach($assembly->libraries as $library){
|
|
|
- //$content .= "<a href=\"/node/$library->node_id\">$library->library_name</a> ";
|
|
|
- //}
|
|
|
- $content .= " </td></tr>".
|
|
|
- "</table>";
|
|
|
-
|
|
|
- # Generate the download linkes
|
|
|
- $a_dir = tripal_get_moddir('tripal_analysis_unigene') .
|
|
|
- "/$assembly->analysis_id";
|
|
|
-
|
|
|
- if(is_dir($a_dir)){
|
|
|
- $content .= "<ul class=\"organism\">";
|
|
|
-
|
|
|
- if($target_file = file_scan_directory($a_dir,'\.contigs.fasta$',
|
|
|
- array('.','..','CVS'),0,FALSE)){
|
|
|
- foreach($target_file as $key=>$value){
|
|
|
- $target = $target_file[$key];
|
|
|
- }
|
|
|
- $link = url($target->filename);
|
|
|
- $content .= "
|
|
|
- <li>
|
|
|
- <a href=\"$link\">Download contigs </a>
|
|
|
- </li>
|
|
|
- ";
|
|
|
- }
|
|
|
- if($target_file = file_scan_directory($a_dir,'\.contigs.qual$',
|
|
|
- array('.','..','CVS'),0,FALSE)){
|
|
|
- foreach($target_file as $key=>$value){
|
|
|
- $target = $target_file[$key];
|
|
|
- }
|
|
|
- $link = url($target->filename);
|
|
|
- $content .= "
|
|
|
- <li>
|
|
|
- <a href=\"$link\">Download contigs quality </a>
|
|
|
- </li>
|
|
|
- ";
|
|
|
- }
|
|
|
- if($target_file = file_scan_directory($a_dir,'\.singlets.fasta$',
|
|
|
- array('.','..','CVS'),0,FALSE)){
|
|
|
- foreach($target_file as $key=>$value){
|
|
|
- $target = $target_file[$key];
|
|
|
- }
|
|
|
- $link = url($target->filename);
|
|
|
- $content .= "
|
|
|
- <li>
|
|
|
- <a href=\"$link\">Download singlets </a>
|
|
|
- </li>
|
|
|
- ";
|
|
|
-
|
|
|
- }
|
|
|
- if($target_file = file_scan_directory($a_dir,'\.singlets.qual$',
|
|
|
- array('.','..','CVS'),0,FALSE)){
|
|
|
- foreach($target_file as $key=>$value){
|
|
|
- $target = $target_file[$key];
|
|
|
- }
|
|
|
- $link = url($target->filename);
|
|
|
- $content .= "
|
|
|
- <li>
|
|
|
- <a href=\"$link\">Download singlets quality </a>
|
|
|
- </li>
|
|
|
- ";
|
|
|
-
|
|
|
- }
|
|
|
- if($target_file = file_scan_directory($a_dir,'\.ace$',
|
|
|
- array('.','..','CVS'),0,FALSE)){
|
|
|
- foreach($target_file as $key=>$value){
|
|
|
- $target = $target_file[$key];
|
|
|
- }
|
|
|
- $link = url($target->filename);
|
|
|
- $content .= "
|
|
|
- <li>
|
|
|
- <a href=\"$link\">Download ace file </a>
|
|
|
- </li>
|
|
|
- ";
|
|
|
-;
|
|
|
- }
|
|
|
- $content .= "</ul>";
|
|
|
- }
|
|
|
- if(user_access('access administrative pages')){
|
|
|
- $link = url("tripal_toggle_box_menu/tripal_analysis_unigene/assembly/$node->nid");
|
|
|
- if(strcmp($box_status,"menu_off")==0){
|
|
|
- $content .= "<a href=\"$link\">Show on menu</a>";
|
|
|
- } else {
|
|
|
- $content .= "<a href=\"$link\">Remove from menu</a>";
|
|
|
- }
|
|
|
- }
|
|
|
- $content .= "</div></div>";
|
|
|
+ $unigenes = array();
|
|
|
+ $i=0;
|
|
|
+ $sql = "SELECT nid FROM {chado_analysis} WHERE analysis_id = %d";
|
|
|
+ while($unigene = db_fetch_object($results)){
|
|
|
+ $analysis_id = $unigene->analysis_id;
|
|
|
+ $c_node = db_fetch_object(db_query($sql,$analysis_id));
|
|
|
+ if($c_node){
|
|
|
+ $unigene->nid = $c_node->nid;
|
|
|
}
|
|
|
-
|
|
|
- $content .= "</div>";
|
|
|
+ // add in the properties
|
|
|
+ $unigene_name = tripal_analysis_get_property($analysis_id,'analysis_unigene_name');
|
|
|
+ $num_contigs = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_contigs');
|
|
|
+ $num_reads = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_reads');
|
|
|
+ $num_clusters = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_clusters');
|
|
|
+ $num_singlets = tripal_analysis_get_property($analysis_id,'analysis_unigene_num_singlets');
|
|
|
+
|
|
|
+ $unigene->unigene_name = $unigene_name[0]->value;
|
|
|
+ $unigene->num_reads = $num_reads[0]->value;
|
|
|
+ $unigene->num_clusters = $num_clusters[0]->value;
|
|
|
+ $unigene->num_contigs = $num_contigs[0]->value;
|
|
|
+ $unigene->num_singlets = $num_singlets[0]->value;
|
|
|
+
|
|
|
+ $unigenes[$i++] = $unigene;
|
|
|
}
|
|
|
- return $content;
|
|
|
+ return $unigenes;
|
|
|
}
|
|
|
/*******************************************************************************
|
|
|
* Tripal Unigene administrative setting form. This function is called by
|
|
|
@@ -648,43 +710,4 @@ function tripal_analysis_unigene_get_settings() {
|
|
|
return $settings;
|
|
|
}
|
|
|
|
|
|
-/*******************************************************************************
|
|
|
- * Set the permission types that the chado module uses. Essentially we
|
|
|
- * want permissionis that protect creation, editing and deleting of chado
|
|
|
- * data objects
|
|
|
- */
|
|
|
-function tripal_analysis_unigene_perm(){
|
|
|
- return array(
|
|
|
- 'access chado_analysis_unigene content',
|
|
|
- 'create chado_analysis_unigene content',
|
|
|
- 'delete chado_analysis_unigene content',
|
|
|
- 'edit chado_analysis_unigene content',
|
|
|
- );
|
|
|
-}
|
|
|
-
|
|
|
-/*******************************************************************************
|
|
|
- * The following function proves access control for users trying to
|
|
|
- * perform actions on data managed by this module
|
|
|
- */
|
|
|
-function chado_analysis_unigene_access($op, $node, $account){
|
|
|
- if ($op == 'create') {
|
|
|
- return user_access('create chado_analysis_unigene content', $account);
|
|
|
- }
|
|
|
|
|
|
- if ($op == 'update') {
|
|
|
- if (user_access('edit chado_analysis_unigene content', $account)) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- }
|
|
|
- if ($op == 'delete') {
|
|
|
- if (user_access('delete chado_analysis_unigene content', $account)) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- }
|
|
|
- if ($op == 'view') {
|
|
|
- if (user_access('access chado_analysis_unigene content', $account)) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- }
|
|
|
- return FALSE;
|
|
|
-}
|
spficklin