Changed all user_access checks to use 'administer tripal' instead of 'access administative pages

tripal_analysis/theme/tripal_analysis/tripal_analysis_base.tpl.php

@@ -72,7 +72,7 @@ $rows[] = array(
 ); 
 
 // allow site admins to see the analysis ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Analysis ID
   $rows[] = array(
     array(

tripal_contact/theme/tripal_contact/tripal_contact_base.tpl.php

@@ -34,7 +34,7 @@ $rows[] = array(
   $contact->type_id->name,
 );
 // allow site admins to see the contact ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Pub ID
   $rows[] = array(
     array(

tripal_feature/includes/tripal_feature.seq_extract.inc

@@ -44,7 +44,7 @@ function tripal_feature_seq_extract_page() {
 
   // generate the search form
   $output .= '';
-  if (user_access('access administration pages')) {
+  if (user_access('administer tripal')) {
     $output .= tripal_set_message("Administrators, the " . 
         l('organism_feature_count', 'admin/tripal/schema/mviews') . " and " .
         l('analysis_organism', 'admin/tripal/schema/mviews') . " materialized

tripal_feature/theme/tripal_feature/tripal_feature_base.tpl.php

@@ -64,7 +64,7 @@ if($feature->seqlen > 0) {
   );
 }
 // allow site admins to see the feature ID
-if (user_access('access administration pages')) { 
+if (user_access('administer tripal')) { 
   // Feature ID
   $rows[] = array(
     array(

tripal_feature/theme/tripal_organism/tripal_organism_feature_counts.tpl.php

@@ -71,7 +71,7 @@ if ($enabled) {
     <img class="tripal_cv_chart" id="tripal_feature_cv_chart_<?php print $organism->organism_id?>" src="" border="0"><?php 
    } 
    else { 
-    if (user_access('access administration pages')) { ?>
+    if (user_access('administer tripal')) { ?>
       <div class="tripal_organism-data-block-desc tripal-data-block-desc">The following data types are currently present for this organism</div> <?php 
       print tripal_set_message("
          Administrators, to view the feature type report:

tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_base.tpl.php

@@ -38,7 +38,7 @@ $rows[] = array(
   $featuremap->unittype_id->name
 );
 // allow site admins to see the feature ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Feature Map ID
   $rows[] = array(
     array(

tripal_library/theme/tripal_library/tripal_library_base.tpl.php

@@ -63,7 +63,7 @@ $rows[] = array(
 );
 
 // allow site admins to see the library ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Library ID
   $rows[] = array(
     array(

tripal_organism/theme/tripal_organism/tripal_organism_base.tpl.php

@@ -63,7 +63,7 @@ $rows[] = array(
 );
 
 // allow site admins to see the organism ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Organism ID
   $rows[] = array(
     array(

tripal_phenotype/tripal_phenotype.views_default.inc

@@ -41,7 +41,7 @@ function tripal_phenotype_defaultview_admin_phenotypes() {
   $handler->display->display_options['title'] = 'Phenotypes';
   $handler->display->display_options['use_more_always'] = FALSE;
   $handler->display->display_options['access']['type'] = 'perm';
-  $handler->display->display_options['access']['perm'] = 'access administration pages';
+  $handler->display->display_options['access']['perm'] = 'administer tripal';
   $handler->display->display_options['cache']['type'] = 'none';
   $handler->display->display_options['query']['type'] = 'views_query';
   $handler->display->display_options['exposed_form']['type'] = 'basic';

tripal_project/theme/tripal_project/tripal_project_base.tpl.php

@@ -47,7 +47,7 @@ $rows[] = array(
   $project->name
 );
 // allow site admins to see the feature ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Project ID
   $rows[] = array(
     array(

tripal_pub/theme/tripal_pub/pub_types/conference_proceedings.inc

@@ -97,7 +97,7 @@ $rows[] = array(
   htmlspecialchars($citation->value)
 );
 // allow site admins to see the pub ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Pub ID
   $rows[] = array(
     array(

tripal_pub/theme/tripal_pub/pub_types/journal_article.inc

@@ -97,7 +97,7 @@ $rows[] = array(
   htmlspecialchars($citation->value)
 );
 // allow site admins to see the pub ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Pub ID
   $rows[] = array(
     array(

tripal_pub/theme/tripal_pub/pub_types/patent.inc

@@ -73,7 +73,7 @@ $rows[] = array(
   htmlspecialchars($citation->value)
 );
 // allow site admins to see the pub ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // Pub ID
   $rows[] = array(
     array(

tripal_pub/theme/tripal_pub/tripal_pub_base.tpl.php

@@ -200,7 +200,7 @@ else {
     htmlspecialchars($citation->value)
   );
   // allow site admins to see the pub ID
-  if (user_access('access administration pages')) {
+  if (user_access('administer tripal')) {
     // Pub ID
     $rows[] = array(
       array(

tripal_stock/theme/tripal_stock/tripal_stock_base.tpl.php

@@ -61,7 +61,7 @@ $rows[] = array(
   $organism
 );
 // allow site admins to see the stock ID
-if (user_access('access administration pages')) {
+if (user_access('administer tripal')) {
   // stock ID
   $rows[] = array(
     array(