Removing CORE Deprecated functions

tripal_core/api/get_FKs.php

@@ -46,7 +46,7 @@ function get_chado_fk_relationships($version) {
   $v = $version;
   $v = preg_replace("/\./","_",$v);
 
-  $tables = tripal_core_get_chado_tables();
+  $tables = chado_get_table_names();
   $sql ="
     SELECT
         tc.constraint_name, tc.table_name, kcu.column_name,
@@ -84,10 +84,10 @@ function get_chado_fk_relationships($version) {
  * the Drupal-style array definition for any table, use the following function
  * call:
  *
- *   \$table_desc = tripal_core_get_chado_table_schema(\$table)
+ *   \$table_desc = chado_get_schema(\$table)
  *
  * where the variable \$table contains the name of the table you want to
- * retireve.  The tripal_core_get_chado_table_schema function determines the appropriate version of
+ * retireve.  The chado_get_schema function determines the appropriate version of
  * Chado and uses the Drupal hook infrastructure to call the appropriate
  * hook function to retrieve the table schema.
  *
@@ -100,7 +100,7 @@ function get_chado_fk_relationships($version) {
   foreach ($tables as $table) {
 
     // get the existing table array
-    $table_arr = tripal_core_get_chado_table_schema($table);
+    $table_arr = chado_get_schema($table);
 
     if (empty($table_arr)) {
        print "ERROR: empty table definition $table\n";
@@ -140,9 +140,9 @@ function get_chado_fk_relationships($version) {
 print "/**
  * Implements hook_chado_schema_v".$v."_".$table."()
  * Purpose: To describe the structure of '$table' to tripal
- * @see tripal_core_chado_insert()
- * @see tripal_core_chado_update()
- * @see tripal_core_chado_select()
+ * @see chado_insert_record()
+ * @see chado_update_record()
+ * @see chado_select_record()
  *
  * @return
  *    An array describing the '$table' table

tripal_example/includes/tripal_example.chado_node.inc

@@ -370,7 +370,7 @@ function chado_example_insert($node) {
   // we do need to proceed with the rest of the insert
   if (!property_exists($node, 'example_id')) {
 
-    // perform the insert using the tripal_core_chado_insert function();
+    // perform the insert using the chado_insert_record function();
     $values = array(
       'uniquename' => $node->uniquename,
       'description' => $node->description,
@@ -574,13 +574,13 @@ function chado_example_load($nodes) {
     // cases it is probably best to let the end-user decide if text fields should
     // be included by using this function in the templates.
     $example = chado_expand_var($example, 'field', 'example.description');
-    
+
 
     // If your module is using the Chado Node: Title & Path API to allow custom titles
     // for your node type. Every time you want the title of the node, you need to use the
     // following API function:
     $node->title = chado_get_node_title($node);
-    
+
     // add the new example object to this node.
     $nodes[$nid]->example = $example;
   }
@@ -653,10 +653,10 @@ function tripal_example_node_insert($node) {
   // it in the hook_insert()
   switch ($node->type) {
     case 'chado_example':
-     
+
       // find the example and add in the details
       $example_id = chado_get_id_from_nid('example', $nid);
-      
+
       // build the example variable by using the chado_generate_var() function
       $values = array('example_id' => $example_id);
       $example = chado_generate_var('example', $values);
@@ -777,9 +777,9 @@ function tripal_example_node_view($node, $view_mode, $langcode) {
           '#tripal_toc_id'    => 'relationships',
           '#tripal_toc_title' => 'Relationships',
         );
-        
-        // Note: if you create a template that you do not want a user to 
-        // know where it is (discourage editing of it), you can add the following 
+
+        // Note: if you create a template that you do not want a user to
+        // know where it is (discourage editing of it), you can add the following
         // key:  '#tripal_template_show' => FALSE. If this key/value is set
         // the the administrator message that Tripal provides indicating
         // where the template is housed will not be shown.

tripal_feature/includes/tripal_feature.chado_node.inc

@@ -775,12 +775,12 @@ function tripal_feature_node_insert($node) {
     case 'chado_feature':
 
       $feature_id = chado_get_id_from_nid('feature', $node->nid);
-      
+
       // build the feature variable
       $values = array('feature_id' => $feature_id);
       $feature = chado_generate_var('feature', $values);
       $node->feature = $feature;
-      
+
       // on an insert we need to add the feature_id to the node object
       // so that the tripal_feature_get_feature_url function can set the URL properly
       $node->feature_id = chado_get_id_from_nid('feature', $node->nid);
@@ -811,14 +811,14 @@ function tripal_feature_node_update($node) {
   // add items to other nodes, build index and search results
   switch ($node->type) {
     case 'chado_feature':
-      
+
       $feature_id = chado_get_id_from_nid('feature', $node->nid);
-      
+
       // build the feature variable
       $values = array('feature_id' => $feature_id);
       $feature = chado_generate_var('feature', $values);
       $node->feature = $feature;
-      
+
       // remove any previous alias
       db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
 
@@ -963,7 +963,7 @@ function tripal_feature_set_urls($na = NULL, $job = NULL) {
       // update the job status every 1% features
       if ($job and $num_set % $num_per_interval == 0) {
         $percent = ($num_set / $num_nodes) * 100;
-        tripal_job_set_progress($job, intval($percent));
+        tripal_set_job_progress($job, intval($percent));
         $percent = sprintf("%.2f", $percent);
         print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
 
@@ -971,7 +971,7 @@ function tripal_feature_set_urls($na = NULL, $job = NULL) {
       $num_set++;
     }
     $percent = ($num_set / $num_nodes) * 100;
-    tripal_job_set_progress($job, intval($percent));
+    tripal_set_job_progress($job, intval($percent));
     $percent = sprintf("%.2f", $percent);
     print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
     print "\nDone. Set " . number_format($num_set) . " URLs\n";

tripal_feature/includes/tripal_feature.gff_loader.inc

@@ -314,62 +314,62 @@ function tripal_feature_gff3_load_form_submit($form, &$form_state) {
  *   Set to 1 if feature should be added only.  In the case where a feature
  *   already exists, it will not be updated.  Default is 0
  * @param $update
- *   Set to 1 to update existing features. New features will be added. Attributes 
- *   for a feature that are not present in the GFF but which are present in the 
+ *   Set to 1 to update existing features. New features will be added. Attributes
+ *   for a feature that are not present in the GFF but which are present in the
  *   database will not be altered. Default is 1
  * @param $refresh
- *   Set to 1 to update existing features. New features will be added. Attributes 
- *   for a feature that are not present in the GFF but which are present in the 
+ *   Set to 1 to update existing features. New features will be added. Attributes
+ *   for a feature that are not present in the GFF but which are present in the
  *   database will be removed. Default is 0
  * @param $remove
- *   Set to 1 to remove features present in the GFF file that exist in the database. 
+ *   Set to 1 to remove features present in the GFF file that exist in the database.
  *   Default is 0.
  * @param $use_transaction
  *   Set to 1 to use a transaction when loading the GFF. Any failure during
  *   loading will result in the rollback of any changes. Default is 1.
  * @param $target_organism_id
- *   If the GFF file contains a 'Target' attribute then the feature and the 
- *   target will have an alignment created, but to find the proper target 
- *   feature the target organism must also be known.  If different from the 
+ *   If the GFF file contains a 'Target' attribute then the feature and the
+ *   target will have an alignment created, but to find the proper target
+ *   feature the target organism must also be known.  If different from the
  *   organism specified for the GFF file, then use  this argument to specify
- *   the target organism.  Only use this argument if all target sequences belong 
- *   to the same species. If the targets in the GFF file belong to multiple 
- *   different species then the organism must be specified using the 
+ *   the target organism.  Only use this argument if all target sequences belong
+ *   to the same species. If the targets in the GFF file belong to multiple
+ *   different species then the organism must be specified using the
  *   'target_organism=genus:species' attribute in the GFF file. Default is NULL.
  * @param $target_type
- *   If the GFF file contains a 'Target' attribute then the feature and the 
- *   target will have an alignment created, but to find the proper target 
- *   feature the target organism must also be known.  This can be used to 
+ *   If the GFF file contains a 'Target' attribute then the feature and the
+ *   target will have an alignment created, but to find the proper target
+ *   feature the target organism must also be known.  This can be used to
  *   specify the target feature type to help with identification of the target
- *   feature.  Only use this argument if all target sequences types are the same. 
- *   If the targets are of different types then the type must be specified using 
- *   the 'target_type=type' attribute in the GFF file. This must be a valid 
+ *   feature.  Only use this argument if all target sequences types are the same.
+ *   If the targets are of different types then the type must be specified using
+ *   the 'target_type=type' attribute in the GFF file. This must be a valid
  *   Sequence Ontology (SO) term. Default is NULL
  * @param $create_target
- *   Set to 1 to create the target feature if it cannot be found in the 
- *   database. Default is 0 
+ *   Set to 1 to create the target feature if it cannot be found in the
+ *   database. Default is 0
  * @param $start_line
  *   Set this to the line in the GFF file where importing should start. This
  *   is useful for testing and debugging GFF files that may have problems and
  *   you want to start at a particular line to speed testing.  Default = 1
  * @param $landmark_type
- *   Use this argument to specify a Sequence Ontology term name for the landmark 
- *   sequences in the GFF fie (e.g. 'chromosome'), if the GFF file contains a 
+ *   Use this argument to specify a Sequence Ontology term name for the landmark
+ *   sequences in the GFF fie (e.g. 'chromosome'), if the GFF file contains a
  *   '##sequence-region' line that describes the landmark sequences. Default = ''
  * @param $alt_id_attr
- *   Sometimes lines in the GFF file are missing the required ID attribute that 
- *   specifies the unique name of the feature. If so, you may specify the 
+ *   Sometimes lines in the GFF file are missing the required ID attribute that
+ *   specifies the unique name of the feature. If so, you may specify the
  *   name of an existing attribute to use for the ID.
  * @param $create_organism
- *   The Tripal GFF loader supports the "organism" attribute. This allows 
- *   features of a different organism to be aligned to the landmark sequence of 
- *   another species. The format of the attribute is "organism=[genus]:[species]", 
- *   where [genus] is the organism's genus and [species] is the species name. 
- *   Check this box to automatically add the organism to the database if it does 
- *   not already exists. Otherwise lines with an oraganism attribute where the 
+ *   The Tripal GFF loader supports the "organism" attribute. This allows
+ *   features of a different organism to be aligned to the landmark sequence of
+ *   another species. The format of the attribute is "organism=[genus]:[species]",
+ *   where [genus] is the organism's genus and [species] is the species name.
+ *   Check this box to automatically add the organism to the database if it does
+ *   not already exists. Otherwise lines with an oraganism attribute where the
  *   organism is not present in the database will be skipped.
  * @param $job
- *  The tripal job_id.  Only used by the Tripal Jobs subsystem. 
+ *  The tripal job_id.  Only used by the Tripal Jobs subsystem.
  *
  * @ingroup gff3_loader
  */
@@ -424,7 +424,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     $sql = "SELECT * FROM {cv} WHERE name = :cvname";
     $cv = chado_query($sql, array(':cvname' => 'sequence'))->fetchObject();
     if (!$cv) {
-      tripal_report_error('T_gff3_loader', TRIPAL_ERROR, 
+      tripal_report_error('T_gff3_loader', TRIPAL_ERROR,
         "Cannot find the 'sequence' ontology", array());
       return '';
     }
@@ -947,7 +947,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     }
   }
   catch (Exception $e) {
-    print "\n"; // make sure we start errors on new line    
+    print "\n"; // make sure we start errors on new line
     if ($use_transaction) {
       $transaction->rollback();
       print "FAILED: Rolling back database changes...\n";
@@ -981,7 +981,7 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
     'organism_id' => $organism->organism_id,
     'uniquename' => $subject,
   );
-  $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values);
+  $result = chado_select_record('tripal_gff_temp', array('type_name'), $values);
   $type_id = array();
   if (count($result) > 0) {
     $type_id = array(
@@ -991,12 +991,12 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
       ),
     );
   }
-  
+
   // if we don't have a subject type then look for the feature in the feature table
   if (empty($type_id)) {
-    $result = tripal_core_chado_select('feature', array('type_id'), $values);
+    $result = chado_select_record('feature', array('type_id'), $values);
     if (count($result) > 1) {
-      watchdog("T_gff3_loader", "Cannot find subject type for feature,'%subject' , in 'derives_from' relationship. Multiple matching features exist with this uniquename.", 
+      watchdog("T_gff3_loader", "Cannot find subject type for feature,'%subject' , in 'derives_from' relationship. Multiple matching features exist with this uniquename.",
         array('%subject' => $subject), WATCHDOG_WARNING);
       return '';
     }
@@ -1562,7 +1562,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
     if (strcmp($score, '.') != 0) {
       $af_values['significance'] = $score;
     }
-    if (!tripal_core_chado_insert('analysisfeature', $af_values)) {
+    if (!chado_insert_record('analysisfeature', $af_values)) {
       tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not add analysisfeature record: $analysis_id, $feature->feature_id", array());
     }
   }

tripal_feature/theme/templates/tripal_organism_feature_browser.tpl.php

@@ -11,7 +11,7 @@ $so_terms = explode(' ', $allowed_types);
 
 // get the feature_id's of the feature that belong to this organism.  But we only
 // want 25 and we want a pager to let the user cycle between pages of features.
-// so we, use the tripal_core_chado_select API function to get the results and
+// so we, use the chado_select_record API function to get the results and
 // generate the pager.  The function is smart enough to know which page the user is
 // on and retrieves the proper set of features
 $element = 0;        // an index to specify the pager if more than one is on the page
@@ -25,12 +25,12 @@ $values = array(
 $columns = array('feature_id');
 $options = array(
   'pager' => array(
-    'limit' => $num_per_page, 
+    'limit' => $num_per_page,
     'element' => $element
    ),
   'order_by' => array('name' => 'ASC'),
 );
-$results = tripal_core_chado_select('feature', $columns, $values, $options);
+$results = chado_select_record('feature', $columns, $values, $options);
 
 // now that we have all of the feature IDs, we want to expand each one so that we
 // have all of the neccessary values, including the node ID, if one exists, and the
@@ -48,18 +48,18 @@ foreach ($results as $result) {
 
 if (count($features) > 0) { ?>
   <div class="tripal_organism-data-block-desc tripal-data-block-desc">The following browser provides a quick view for new visitors.  Use the searching mechanism to find specific features.</div> <?php
-  
+
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Feature Name' ,'Unique Name', 'Type');
-  
+
   // the $rows array contains an array of rows where each row is an array
   // of values for each column of the table in that row.  Additional documentation
   // can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
-  
+
   // let admins know they can customize the terms that appear in the list
   print tripal_set_message("Administrators, you can specify the feature types ".
     "that should appear in this browser or remove it from the list of resources ".
@@ -68,7 +68,7 @@ if (count($features) > 0) { ?>
     TRIPAL_INFO,
     array('return_html' => 1)
   );
-  
+
   foreach ($features as $feature){
     $fname =  $feature->name;
     if (property_exists($feature, 'nid')) {
@@ -79,7 +79,7 @@ if (count($features) > 0) { ?>
       $feature->uniquename,
       $feature->type_id->name
     );
-  } 
+  }
   // the $table array contains the headers and rows array as well as other
   // options for controlling the display of the table.  Additional
   // documentation can be found here:
@@ -99,8 +99,8 @@ if (count($features) > 0) { ?>
   // once we have our table array structure defined, we call Drupal's theme_table()
   // function to generate the table.
   print theme_table($table);
-  
-  // the $pager array values that control the behavior of the pager.  For 
+
+  // the $pager array values that control the behavior of the pager.  For
   // documentation on the values allows in this array see:
   // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
   // here we add the paramter 'block' => 'feature_browser'. This is because
@@ -114,8 +114,8 @@ if (count($features) > 0) { ?>
     ),
     'quantity' => $num_per_page,
   );
-  print theme_pager($pager); 
-} 
+  print theme_pager($pager);
+}
 else {  ?>
   <p>There are no results.</p><?php
   print tripal_set_message("
@@ -134,7 +134,7 @@ else {  ?>
     <br>
     <br>
     You can specify the feature types
-    that should appear in this browser or remove it from the list of resources by navigating to the " . 
+    that should appear in this browser or remove it from the list of resources by navigating to the " .
     l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank')))  . "
     The feature browser will not appear to site visitors unless features are present. ",
     TRIPAL_INFO,

tripal_library/theme/templates/tripal_library_features.tpl.php

@@ -4,7 +4,7 @@ $library = $variables['node']->library;
 
 // get the feature_id's of the features that belong to this library.  But we only
 // want 25 and we want a pager to let the user cycle between pages of features.
-// so we, use the tripal_core_chado_select API function to get the results and
+// so we, use the chado_select_record API function to get the results and
 // generate the pager.  The function is smart enough to know which page the user is
 // on and retrieves the proper set of features
 $element = 0;        // an index to specify the pager if more than one is on the page
@@ -15,11 +15,11 @@ $values = array(
 $columns = array('feature_id');
 $options = array(
   'pager' => array(
-    'limit' => $num_per_page, 
+    'limit' => $num_per_page,
     'element' => $element
    ),
 );
-$results = tripal_core_chado_select('library_feature', $columns, $values, $options);
+$results = chado_select_record('library_feature', $columns, $values, $options);
 
 // now that we have all of the feature IDs, we want to expand each one so that we
 // have all of the neccessary values, including the node ID, if one exists, and the
@@ -37,12 +37,12 @@ foreach ($results as $library_feature) {
 
 if (count($features) > 0) { ?>
   <div class="tripal_library-data-block-desc tripal-data-block-desc">The following browser provides a quick view for new visitors.  Use the searching mechanism to find specific features.</div> <?php
-  
+
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Feature Name' ,'Unique Name', 'Type');
-  
+
   // the $rows array contains an array of rows where each row is an array
   // of values for each column of the table in that row.  Additional documentation
   // can be found here:
@@ -59,7 +59,7 @@ if (count($features) > 0) { ?>
       $feature->uniquename,
       $feature->type_id->name
     );
-  } 
+  }
   // the $table array contains the headers and rows array as well as other
   // options for controlling the display of the table.  Additional
   // documentation can be found here:
@@ -79,8 +79,8 @@ if (count($features) > 0) { ?>
   // once we have our table array structure defined, we call Drupal's theme_table()
   // function to generate the table.
   print theme_table($table);
-  
-  // the $pager array values that control the behavior of the pager.  For 
+
+  // the $pager array values that control the behavior of the pager.  For
   // documentation on the values allows in this array see:
   // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
   // here we add the paramter 'block' => 'feature_browser'. This is because
@@ -94,8 +94,8 @@ if (count($features) > 0) { ?>
     ),
     'quantity' => $num_per_page,
   );
-  print theme_pager($pager); 
-} 
+  print theme_pager($pager);
+}
 
 
 

tripal_project/includes/tripal_project.chado_node.inc

@@ -404,7 +404,7 @@ function chado_project_load($nodes) {
 
     // Now get the title
     $node->title = chado_get_node_title($node);
-      
+
   }
 
 }
@@ -524,7 +524,7 @@ function tripal_project_node_insert($node) {
   // know the project_id in the presave
   switch ($node->type) {
     case 'chado_project':
-      
+
       // get the feature details from chado
       $project_id = chado_get_id_from_nid('project', $node->nid);
       $values = array('project_id' => $project_id);
@@ -533,7 +533,7 @@ function tripal_project_node_insert($node) {
 
       // Now get the title
       $node->title = chado_get_node_title($node);
-      
+
       // on an insert we need to add the project_id to the node object
       // so that the tripal_project_get_project_url function can set the URL properly
       $node->project_id = $project_id;
@@ -566,10 +566,10 @@ function tripal_project_node_update($node) {
       $values = array('project_id' => $project_id);
       $project = chado_generate_var('project', $values);
       $nodes->project = $project;
-      
+
       // Now get the title
       $node->title = chado_get_node_title($node);
-      
+
       // remove any previous alias
       db_query("DELETE FROM {url_alias} WHERE source = :source", array(':source' => "node/$node->nid"));
 
@@ -694,7 +694,7 @@ function tripal_project_set_urls($na = NULL, $job = NULL) {
       // update the job status every 1% projects
       if ($job and $num_set % $num_per_interval == 0) {
         $percent = ($num_set / $num_nodes) * 100;
-        tripal_job_set_progress($job, intval($percent));
+        tripal_set_job_progress($job, intval($percent));
         $percent = sprintf("%.2f", $percent);
         print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
 
@@ -702,7 +702,7 @@ function tripal_project_set_urls($na = NULL, $job = NULL) {
       $num_set++;
     }
     $percent = ($num_set / $num_nodes) * 100;
-    tripal_job_set_progress($job, intval($percent));
+    tripal_set_job_progress($job, intval($percent));
     $percent = sprintf("%.2f", $percent);
     print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
     print "\nDone. Set " . number_format($num_set) . " URLs\n";

tripal_pub/theme/templates/tripal_pub_featuremaps.tpl.php

@@ -4,18 +4,18 @@ $featuremaps = array();
 
 // get the featuremaps that are associated with this publication.  But we only
 // want 25 and we want a pager to let the user cycle between pages of featuremaps.
-// so we, use the tripal_core_chado_select API function to get the results and
+// so we, use the chado_select_record API function to get the results and
 // generate the pager.  The function is smart enough to know which page the user is
 // on and retrieves the proper set of featuremaps
 
 $element = 1;        // an index to specify the pager this must be unique amongst all pub templates
-$num_per_page = 25;  // the number of featuremaps to show per page$num_results_per_page = 25; 
+$num_per_page = 25;  // the number of featuremaps to show per page$num_results_per_page = 25;
 
 // get the featuremaps from the featuremap_pub table
-$options = array(  
+$options = array(
   'return_array' => 1,
   'pager' => array(
-    'limit'   => $num_per_page, 
+    'limit'   => $num_per_page,
     'element' => $element
   ),
 );
@@ -23,7 +23,7 @@ $options = array(
 $pub = chado_expand_var($pub, 'table', 'featuremap_pub', $options);
 $featuremap_pubs = $pub->featuremap_pub;
 if (count($featuremap_pubs) > 0 ) {
-  foreach ($featuremap_pubs as $featuremap_pub) {    
+  foreach ($featuremap_pubs as $featuremap_pub) {
     $featuremaps[] = $featuremap_pub->featuremap_id;
   }
 }
@@ -32,25 +32,25 @@ if (count($featuremap_pubs) > 0 ) {
 $total_records = chado_pager_get_count($element);
 
 if(count($featuremaps) > 0){ ?>
-  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> maps:</div> <?php 
+  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> maps:</div> <?php
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Map Name');
-  
+
   // the $rows array contains an array of rows where each row is an array
   // of values for each column of the table in that row.  Additional documentation
   // can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
-  
+
   foreach ($featuremaps as $featuremap){
      $featuremap_name = $featuremap->name;
      if (property_exists($featuremap, 'nid')) {
        $featuremap_name = l($featuremap_name, 'node/' . $featuremap->nid, array('attributes' => array('target' => '_blank')));
      }
-     
+
      $rows[] = array(
        $featuremap_name,
      );
@@ -74,7 +74,7 @@ if(count($featuremaps) > 0){ ?>
   // once we have our table array structure defined, we call Drupal's theme_table()
   // function to generate the table.
   print theme_table($table);
-  
+
   // the $pager array values that control the behavior of the pager.  For
   // documentation on the values allows in this array see:
   // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
@@ -89,6 +89,6 @@ if(count($featuremaps) > 0){ ?>
     ),
     'quantity' => $num_per_page,
   );
-  print theme_pager($pager); 
+  print theme_pager($pager);
 }?>
 

tripal_pub/theme/templates/tripal_pub_features.tpl.php

@@ -4,18 +4,18 @@ $features = array();
 
 // get the features that are associated with this publication.  But we only
 // want 25 and we want a pager to let the user cycle between pages of features.
-// so we, use the tripal_core_chado_select API function to get the results and
+// so we, use the chado_select_record API function to get the results and
 // generate the pager.  The function is smart enough to know which page the user is
 // on and retrieves the proper set of features
 
 $element = 2;        // an index to specify the pager this must be unique amongst all pub templates
-$num_per_page = 25;  // the number of features to show per page$num_results_per_page = 25; 
+$num_per_page = 25;  // the number of features to show per page$num_results_per_page = 25;
 
 // get the features from the feature_pub table
-$options = array(  
+$options = array(
   'return_array' => 1,
   'pager' => array(
-    'limit'   => $num_per_page, 
+    'limit'   => $num_per_page,
     'element' => $element
   ),
 );
@@ -23,7 +23,7 @@ $options = array(
 $pub = chado_expand_var($pub, 'table', 'feature_pub', $options);
 $feature_pubs = $pub->feature_pub;
 if (count($feature_pubs) > 0 ) {
-  foreach ($feature_pubs as $feature_pub) {    
+  foreach ($feature_pubs as $feature_pub) {
     $features[] = $feature_pub->feature_id;
   }
 }
@@ -32,25 +32,25 @@ if (count($feature_pubs) > 0 ) {
 $total_records = chado_pager_get_count($element);
 
 if(count($features) > 0){ ?>
-  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> features:</div> <?php 
+  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> features:</div> <?php
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Feature Name', 'Uniquenaem', 'Type');
-  
+
   // the $rows array contains an array of rows where each row is an array
   // of values for each column of the table in that row.  Additional documentation
   // can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
-  
+
   foreach ($features as $feature){
      $feature_name = $feature->name;
      if (property_exists($feature, 'nid')) {
        $feature_name = l($feature_name, 'node/' . $feature->nid, array('attributes' => array('target' => '_blank')));
      }
-     
+
      $rows[] = array(
        $feature_name,
        $feature->uniquename,
@@ -76,7 +76,7 @@ if(count($features) > 0){ ?>
   // once we have our table array structure defined, we call Drupal's theme_table()
   // function to generate the table.
   print theme_table($table);
-  
+
   // the $pager array values that control the behavior of the pager.  For
   // documentation on the values allows in this array see:
   // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
@@ -91,6 +91,6 @@ if(count($features) > 0){ ?>
     ),
     'quantity' => $num_per_page,
   );
-  print theme_pager($pager);  
+  print theme_pager($pager);
 }
 

tripal_pub/theme/templates/tripal_pub_libraries.tpl.php

@@ -4,18 +4,18 @@ $libraries = array();
 
 // get the libraries that are associated with this publication.  But we only
 // want 25 and we want a pager to let the user cycle between pages of libraries.
-// so we, use the tripal_core_chado_select API function to get the results and
+// so we, use the chado_select_record API function to get the results and
 // generate the pager.  The function is smart enough to know which page the user is
 // on and retrieves the proper set of libraries
 
 $element = 3;        // an index to specify the pager this must be unique amongst all pub templates
-$num_per_page = 25;  // the number of libraries to show per page$num_results_per_page = 25; 
+$num_per_page = 25;  // the number of libraries to show per page$num_results_per_page = 25;
 
 // get the libraries from the library_pub table
-$options = array(  
+$options = array(
   'return_array' => 1,
   'pager' => array(
-    'limit'   => $num_per_page, 
+    'limit'   => $num_per_page,
     'element' => $element
   ),
 );
@@ -23,7 +23,7 @@ $options = array(
 $pub = chado_expand_var($pub, 'table', 'library_pub', $options);
 $library_pubs = $pub->library_pub;
 if (count($library_pubs) > 0 ) {
-  foreach ($library_pubs as $library_pub) {    
+  foreach ($library_pubs as $library_pub) {
     $libraries[] = $library_pub->library_id;
   }
 }
@@ -32,19 +32,19 @@ if (count($library_pubs) > 0 ) {
 $total_records = chado_pager_get_count($element);
 
 if(count($libraries) > 0){ ?>
-  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> libraries:</div> <?php 
+  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> libraries:</div> <?php
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Library Name', 'Unique Name', 'Organism');
-  
+
   // the $rows array contains an array of rows where each row is an array
   // of values for each column of the table in that row.  Additional documentation
   // can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
-  
+
   foreach ($libraries as $library){
      $library_name = $library->name;
      if (property_exists($library, 'nid')) {
@@ -79,7 +79,7 @@ if(count($libraries) > 0){ ?>
   // once we have our table array structure defined, we call Drupal's theme_table()
   // function to generate the table.
   print theme_table($table);
-  
+
   // the $pager array values that control the behavior of the pager.  For
   // documentation on the values allows in this array see:
   // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
@@ -94,6 +94,6 @@ if(count($libraries) > 0){ ?>
     ),
     'quantity' => $num_per_page,
   );
-  print theme_pager($pager); 
+  print theme_pager($pager);
 }
 

tripal_pub/theme/templates/tripal_pub_projects.tpl.php

@@ -4,18 +4,18 @@ $projects = array();
 
 // get the features that are associated with this publication.  But we only
 // want 25 and we want a pager to let the user cycle between pages of features.
-// so we, use the tripal_core_chado_select API function to get the results and
+// so we, use the chado_select_record API function to get the results and
 // generate the pager.  The function is smart enough to know which page the user is
 // on and retrieves the proper set of features
 
 $element = 4;        // an index to specify the pager this must be unique amongst all pub templates
-$num_per_page = 25;  // the number of projects to show per page$num_results_per_page = 25; 
+$num_per_page = 25;  // the number of projects to show per page$num_results_per_page = 25;
 
 // get the projects from the project_pub table
-$options = array(  
+$options = array(
   'return_array' => 1,
   'pager' => array(
-    'limit'   => $num_per_page, 
+    'limit'   => $num_per_page,
     'element' => $element
   ),
 );
@@ -23,7 +23,7 @@ $options = array(
 $pub = chado_expand_var($pub, 'table', 'project_pub', $options);
 $project_pubs = $pub->project_pub;
 if (count($project_pubs) > 0 ) {
-  foreach ($project_pubs as $project_pub) {    
+  foreach ($project_pubs as $project_pub) {
     $projects[] = $project_pub->project_id;
   }
 }
@@ -32,19 +32,19 @@ if (count($project_pubs) > 0 ) {
 $total_records = chado_pager_get_count($element);
 
 if(count($projects) > 0){ ?>
-  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> projects:</div> <?php 
+  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> projects:</div> <?php
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Project Name', 'Description');
-  
+
   // the $rows array contains an array of rows where each row is an array
   // of values for each column of the table in that row.  Additional documentation
   // can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
-  
+
   foreach ($projects as $project){
      $project_name = $project->name;
      if (property_exists($project, 'nid')) {
@@ -53,7 +53,7 @@ if(count($projects) > 0){ ?>
      $description =  substr($project->description, 0, 200);
      if (strlen($project->description) > 200) {
        $description .= "... " . l("[more]", 'node/' . $project->nid, array('attributes' => array('target' => '_blank')));
-     } 
+     }
      $rows[] = array(
        $project_name,
        $description
@@ -78,7 +78,7 @@ if(count($projects) > 0){ ?>
   // once we have our table array structure defined, we call Drupal's theme_table()
   // function to generate the table.
   print theme_table($table);
-  
+
   // the $pager array values that control the behavior of the pager.  For
   // documentation on the values allows in this array see:
   // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
@@ -93,6 +93,6 @@ if(count($projects) > 0){ ?>
     ),
     'quantity' => $num_per_page,
   );
-  print theme_pager($pager);  
+  print theme_pager($pager);
 }
 

tripal_pub/theme/templates/tripal_pub_stocks.tpl.php

@@ -4,18 +4,18 @@ $stocks = array();
 
 // get the stocks that are associated with this publication.  But we only
 // want 25 and we want a pager to let the user cycle between pages of stocks.
-// so we, use the tripal_core_chado_select API function to get the results and
+// so we, use the chado_select_record API function to get the results and
 // generate the pager.  The function is smart enough to know which page the user is
 // on and retrieves the proper set of stocks
 
 $element = 5;        // an index to specify the pager this must be unique amongst all pub templates
-$num_per_page = 25;  // the number of stocks to show per page$num_results_per_page = 25; 
+$num_per_page = 25;  // the number of stocks to show per page$num_results_per_page = 25;
 
 // get the stocks from the stock_pub table
-$options = array(  
+$options = array(
   'return_array' => 1,
   'pager' => array(
-    'limit'   => $num_per_page, 
+    'limit'   => $num_per_page,
     'element' => $element
   ),
 );
@@ -23,7 +23,7 @@ $options = array(
 $pub = chado_expand_var($pub, 'table', 'stock_pub', $options);
 $stock_pubs = $pub->stock_pub;
 if (count($stock_pubs) > 0 ) {
-  foreach ($stock_pubs as $stock_pub) {    
+  foreach ($stock_pubs as $stock_pub) {
     $stocks[] = $stock_pub->stock_id;
   }
 }
@@ -32,25 +32,25 @@ if (count($stock_pubs) > 0 ) {
 $total_records = chado_pager_get_count($element);
 
 if(count($stocks) > 0){ ?>
-  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> stocks:</div> <?php 
+  <div class="tripal_pub-data-block-desc tripal-data-block-desc">This publication contains information about <?php print number_format($total_records) ?> stocks:</div> <?php
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $headers = array('Stock Name', 'Uniquenaem', 'Type');
-  
+
   // the $rows array contains an array of rows where each row is an array
   // of values for each column of the table in that row.  Additional documentation
   // can be found here:
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
   $rows = array();
-  
+
   foreach ($stocks as $stock){
      $stock_name = $stock->name;
      if (property_exists($stock, 'nid')) {
        $stock_name = l($stock_name, 'node/' . $stock->nid, array('attributes' => array('target' => '_blank')));
      }
-     
+
      $rows[] = array(
        $stock_name,
        $stock->uniquename,
@@ -76,7 +76,7 @@ if(count($stocks) > 0){ ?>
   // once we have our table array structure defined, we call Drupal's theme_table()
   // function to generate the table.
   print theme_table($table);
-  
+
   // the $pager array values that control the behavior of the pager.  For
   // documentation on the values allows in this array see:
   // https://api.drupal.org/api/drupal/includes!pager.inc/function/theme_pager/7
@@ -91,6 +91,6 @@ if(count($stocks) > 0){ ?>
     ),
     'quantity' => $num_per_page,
   );
-  print theme_pager($pager); 
+  print theme_pager($pager);
 }
 

tripal_stock/includes/tripal_stock.chado_node.inc

@@ -472,7 +472,7 @@ function chado_stock_insert($node) {
           'db_id' => $node->database,
           'accession' => $node->accession,
         );
-        if (!tripal_core_chado_select('dbxref', array('dbxref_id'), $values)) {
+        if (!chado_select_record('dbxref', array('dbxref_id'), $values)) {
           $values['description'] = $node->db_description;
           $values['version'] = '1';
           $dbxref_status = chado_insert_record('dbxref', $values);
@@ -888,7 +888,7 @@ function tripal_stock_node_insert($node) {
   // know the stock_id in the presave
   switch ($node->type) {
     case 'chado_stock':
-      
+
       // get the feature details from chado
       $stock_id = chado_get_id_from_nid('stock', $node->nid);
       $values = array('stock_id' => $stock_id);
@@ -928,7 +928,7 @@ function tripal_stock_node_update($node) {
   // add items to other nodes, build index and search results
   switch ($node->type) {
     case 'chado_stock':
-      
+
       // get the feature details from chado
       $stock_id = chado_get_id_from_nid('stock', $node->nid);
       $values = array('stock_id' => $stock_id);
@@ -1081,7 +1081,7 @@ function tripal_stock_set_urls($na = NULL, $job = NULL) {
       // update the job status every 1% stocks
       if ($job and $num_set % $num_per_interval == 0) {
         $percent = ($num_set / $num_nodes) * 100;
-        tripal_job_set_progress($job, intval($percent));
+        tripal_set_job_progress($job, intval($percent));
         $percent = sprintf("%.2f", $percent);
         print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
 
@@ -1089,7 +1089,7 @@ function tripal_stock_set_urls($na = NULL, $job = NULL) {
       $num_set++;
     }
     $percent = ($num_set / $num_nodes) * 100;
-    tripal_job_set_progress($job, intval($percent));
+    tripal_set_job_progress($job, intval($percent));
     $percent = sprintf("%.2f", $percent);
     print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
     print "\nDone. Set " . number_format($num_set) . " URLs\n";

tripal_views/tripal_views.views.inc

@@ -554,7 +554,7 @@ function tripal_views_views_data_alter(&$data) {
       $base_title = ucwords(str_replace('_', ' ', $base_table));
 
       // add in joins to the node tables if the Chado schema is local
-      if (tripal_core_chado_schema_exists()) {
+      if (chado_is_local()) {
         // if a node linking table exists then add in the joins
         if (db_table_exists($linker_table)) {