used new property API for analysis module

tripal_analysis/includes/tripal_analysis.form.inc

@@ -183,26 +183,10 @@ function chado_analysis_form($node, &$form_state) {
        someone to recreate the analysis, including materials and methods
        for collection of the source data and performing the analysis'),
   );
-  $form['properties'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Analysis Details'),
-    '#description' => t('You may add additional properties by
-      selecting a property type from the dropdown and adding text.  You may add 
-      as many properties as desired by clicking the add button on the right.  To 
-      remove a property, click the minus button.  If a property is not available
-      you may add it by ' . l('adding the term', 'admin/tripal/tripal_cv/cvterm/add') . '
-      to the <b>analysis_property</b> vocabulary within the <b>tripal</b> database'),
-  );
-  $form['properties']['table'] = array(
-    '#type' => 'markup',
-    '#value' =>  '',
-    '#prefix' => '<div id="tripal-analysis-edit-properties-table">',
-    '#suffix' => '</div>',
-  );
   
   // get the analysis properties
-  $properties_select = array();
-  $properties_select[] = 'Select a Property';
+  $properties = array();
+  $properties[] = 'Select a Property';
   $sql = "
     SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
     FROM  {cvterm} CVT
@@ -214,352 +198,16 @@ function chado_analysis_form($node, &$form_state) {
   ";
   $prop_types = chado_query($sql);
   while ($prop = $prop_types->fetchObject()) {
-    $properties_select[$prop->cvterm_id] = $prop->name;
-  }
-  
-  // this array keeps track of all properties we have and allows the functions
-  // below to select the next rank if a property is dupliated
-  $ranks = array();
- 
-  // add in the properties from the Chado analysisprop table (only pertains to existing analyses)
-  if ($analysis_id) {
-    chado_analysis_node_form_add_analysisprop_table_props($form, $form_state, $analysis_id, $ranks, $d_removed);
+    $properties[$prop->cvterm_id] = $prop->name;
   }
   
-  // add in any new properties that have been added by the user through an AHAH callback
-  chado_analysis_node_form_add_new_props($form, $form_state, $ranks, $d_removed);
+  $exclude = array();
+  $instructions = t('To add additional properties to the drop down. ' . l("Add terms to the analysis_property vocabulary", "admin/tripal/chado/tripal_cv/cvterm/add") . ".");
+  tripal_core_properties_form($form, $form_state, 'analysisprop', 'analysis_id', 'analysis_property',
+    $properties, $analysis_id, $exclude, $instructions);
 
-  // add an empty row of field to allow for addition of a new property
-  chado_analysis_node_form_add_new_empty_props($form, $form_state, $properties_select);
-  
-  $form['#theme'] = 'chado_analysis_form';
   return $form;
 }
-/**
- * This function is responsible for adding a blank row to the properties table for
- * adding a new property.
- */
-function chado_analysis_node_form_add_new_empty_props(&$form, &$form_state, $properties_select) {
-
-  // get the field defaults either from $form_state['values'] or $form_state['input']
-  $description = '';
-  $text = '';
-  $id = 0;
-  if (array_key_exists('values', $form_state)) {
-    $id = $form_state['values']['new_id'];
-    $text = $form_state['values']['new_value'];
-  }
-  
-  // if we have a property ID then get it's definition to display to the user
-  if($id) { 
-    $values = array('cvterm_id' => $id);
-    $cvterm = tripal_core_chado_select('cvterm', array('definition'), $values);
-  
-    if ($cvterm[0]->definition) {
-      $description = $cvterm[0]->definition;
-    }
-  }
-  $rows = 1;
-  
-  // add one more blank set of property fields
-  $form['properties']['table']['new']["new_id"] = array(
-    '#type'          => 'select',
-    '#options'       => $properties_select,
-    '#default_value' => $id,
-    '#ajax' => array(
-      'callback' => "tripal_analysis_property_get_description",
-      'wrapper'  => 'tripal-analysis-new_value',
-      'effect'   => 'fade',
-      'method'   => 'replace',
-    ),
-  );
-  $form['properties']['table']['new']["new_value"] = array(
-    '#type'           => 'textarea',
-    '#default_value'  => $text,
-    '#cols'           => 50,
-    '#rows'           => $rows,
-    '#prefix'         => '<div id="tripal-analysis-new_value">',
-    '#description'    => $description,
-    '#suffix'         => '</div>',
-  );
-  
-  $form['properties']['table']['new']["add"] = array(
-    '#type'    => 'button',
-    '#value'   => t('Add'),
-    '#name'    => 'add',
-    '#ajax'      => array(
-      'callback' => "tripal_analysis_property_ajax_update",
-      'wrapper'  => 'tripal-analysis-edit-properties-table',
-      'effect'   => 'fade',
-      'method'   => 'replace',
-      'prevent'  => 'click'
-    ),
-    // When this button is clicked, the form will be validated and submitted. 
-    // Therefore, we set custom submit and validate functions to override the
-    // default form submit.  In the validate function we set the form_state
-    // to rebuild the form so the submit function never actually gets called,
-    // but we need it or Drupal will run the default validate anyway.
-    // we also set #limit_validation_errors to empty so fields that
-    // are required that don't have values won't generate warnings. 
-    '#submit'   => array('chado_analysis_node_form_props_button_submit'),
-    '#validate' => array('chado_analysis_node_form_props_button_validate'),
-    '#limit_validation_errors' => array(array('new_id')),
-  );
-}
-/**
- * This function is used to rebuild the form if an ajax call is made vai a button.
- * The button causes the form to be submitted. We don't want this so we override
- * the validate and submit routines on the form button. Therefore, this function
- * only needs to tell Drupal to rebuild the form
- */
-function chado_analysis_node_form_props_button_validate($form, &$form_state){
-  if (array_key_exists('triggering_element', $form_state) and 
-      $form_state['triggering_element']['#name'] == 'add' and
-      $form_state['input']['new_id'] == 0 ){
-    form_set_error('new_id', "Please specify a property type");
-    return;
-  }
-  $form_state['rebuild'] = TRUE; 
-}
-/**
- * This function is just a dummy to override the default form submit on ajax calls for buttons
- */
-function chado_analysis_node_form_props_button_submit($form, &$form_state){
-  // do nothing
-}
-/**
- * This adds 
- */
-function chado_analysis_node_form_add_new_props(&$form, &$form_state, &$ranks, &$d_removed) {
-   
-  // set some default values
-  $j = 0;
-  $num_properties = 0;
-  
-  $values = array();
-  if (array_key_exists('values', $form_state)) {
-    $values = $form_state['values'];
-  }
-  if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
-    $values = $form_state['input'];
-  }
-  
-  // first, add in all of the new properties that were added previously via this form
-  foreach ($values as $element_name => $value) {
-    if (preg_match('/new_value-(\d+)-(\d+)/', $element_name, $matches)) {
-      $new_id = $matches[1];
-      $rank = $matches[2];
-  
-      // skip any properties that the user requested to delete through a previous
-      // ajax callback or through the current ajax callback
-      if (array_key_exists("$new_id-$rank", $d_removed)) {
-        continue;
-      }
-      if (array_key_exists('triggering_element', $form_state) and 
-         $form_state['triggering_element']['#name'] == 'remove-' . $new_id . '-' . $rank) {
-        $d_removed["$new_id-$rank"] = 1;
-        continue;
-      }
-  
-      // get this new_id information
-      $args = array('cvterm_id' => $new_id);
-      $cvterm = tripal_core_chado_select('cvterm', array('name', 'definition'), $args);
-
-      // add it to the $ranks array
-      $ranks[$new_id][$rank]['name']  = $cvterm[0]->name;
-      $ranks[$new_id][$rank]['id']    = $new_id;
-      $ranks[$new_id][$rank]['value'] = $value;
-      $ranks[$new_id][$rank]['definition']  = $cvterm[0]->definition;
-      $num_properties++;
-  
-      // determine how many rows we need in the textarea
-      $rows = 1;
-      // add the new fields
-      $form['properties']['table']['new'][$new_id][$rank]["new_id-$new_id-$rank"] = array(
-        '#markup' => $cvterm[0]->name
-      );
-      $form['properties']['table']['new'][$new_id][$rank]["new_value-$new_id-$rank"] = array(
-        '#type'          => 'textarea',
-        '#default_value' => $value,
-        '#cols'          => 50,
-        '#rows'          => $rows,
-        '#description'   => $cvterm[0]->definition,
-      );
-  
-      $form['properties']['table']['new'][$new_id][$rank]["remove-$new_id-$rank"] = array(
-        '#type'         => 'button',
-        '#value'        => t('Remove'),
-        '#name'         => "remove-$new_id-$rank",
-        '#ajax' => array(
-          'callback' => "tripal_analysis_property_ajax_update",
-          'wrapper'  => 'tripal-analysis-edit-properties-table',
-          'effect'   => 'fade',
-          'event'    => 'mousedown',
-          'method'   => 'replace',
-          'prevent'  => 'click'
-        ),
-        // When this button is clicked, the form will be validated and submitted.
-        // Therefore, we set custom submit and validate functions to override the
-        // default form submit.  In the validate function we set the form_state
-        // to rebuild the form so the submit function never actually gets called,
-        // but we need it or Drupal will run the default validate anyway.
-        // we also set #limit_validation_errors to empty so fields that
-        // are required that don't have values won't generate warnings.
-        '#submit'   => array('chado_analysis_node_form_props_button_submit'),
-        '#validate' => array('chado_analysis_node_form_props_button_validate'),
-        '#limit_validation_errors' => array(),
-      );
-    }
-  }
-
-  // second add in any new properties added during this callback 
-  if (array_key_exists('triggering_element', $form_state) and 
-      $form_state['triggering_element']['#name'] == 'add' and
-      $form_state['input']['new_id'] != 0) {
-    $new_id    = $form_state['input']['new_id'];
-    $new_value = $form_state['input']['new_value'];    
-
-    // get the rank by counting the number of entries
-    $rank = count($ranks[$new_id]);
-
-    // get this new_id information
-    $cvterm = tripal_core_chado_select('cvterm', array('name', 'definition'), array('cvterm_id' => $new_id));
-
-    // add it to the $ranks array
-    $ranks[$new_id][$rank]['name']  = $cvterm[0]->name;
-    $ranks[$new_id][$rank]['id']    = $new_id;
-    $ranks[$new_id][$rank]['value'] = $value;
-    $ranks[$new_id][$rank]['definition']  = $cvterm[0]->definition;
-    $num_properties++;
-
-    // determine how many rows we need in the textarea
-    $rows = 1;
-
-    // add the new fields
-    $form['properties']['table']['new'][$new_id][$rank]["new_id-$new_id-$rank"] = array(
-      '#markup' => $cvterm[0]->name
-    );
-    $form['properties']['table']['new'][$new_id][$rank]["new_value-$new_id-$rank"] = array(
-      '#type'          => 'textarea',
-      '#default_value' => $new_value,
-      '#cols'          => 50,
-      '#rows'          => $rows,
-      '#description'   => $cvterm[0]->definition,
-    );
-
-    $form['properties']['table']['new'][$new_id][$rank]["remove-$new_id-$rank"] = array(
-      '#type'         => 'button',
-      '#value'        => t('Remove'),
-      '#name'         => "remove-$new_id-$rank",
-      '#ajax' => array(
-        'callback' => "tripal_analysis_property_ajax_update",
-        'wrapper'  => 'tripal-analysis-edit-properties-table',
-        'effect'   => 'fade',
-        'event'    => 'mousedown',
-        'method'   => 'replace',
-        'prevent'  => 'click'
-      ),
-      // When this button is clicked, the form will be validated and submitted.
-      // Therefore, we set custom submit and validate functions to override the
-      // default form submit.  In the validate function we set the form_state
-      // to rebuild the form so the submit function never actually gets called,
-      // but we need it or Drupal will run the default validate anyway.
-      // we also set #limit_validation_errors to empty so fields that
-      // are required that don't have values won't generate warnings.
-      '#submit'   => array('chado_analysis_node_form_props_button_submit'),
-      '#validate' => array('chado_analysis_node_form_props_button_validate'),
-      '#limit_validation_errors' => array(),
-    );
-
-  }
-
-  return $num_properties;
-}
-/*
- *
-*/
-function chado_analysis_node_form_add_analysisprop_table_props(&$form, $form_state, $analysis_id, &$ranks, &$d_removed) {
-
-  // get the properties for this analysis
-  $num_properties = 0;
-
-  if (!$analysis_id) {
-    return $num_properties;
-  }
-
-  $sql = "
-    SELECT CVT.cvterm_id, CVT.name, CVT.definition, PP.value, PP.rank
-    FROM {analysisprop} PP
-      INNER JOIN {cvterm} CVT on CVT.cvterm_id = PP.type_id
-      INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
-    WHERE PP.analysis_id = :analysis_id and CV.name = 'analysis_property'
-    ORDER BY CVT.name, PP.rank
-  ";
-  $analysis_props = chado_query($sql, array(':analysis_id' => $analysis_id));
-  while ($prop = $analysis_props->fetchObject()) {
-
-    $type_id = $prop->cvterm_id;
-    $rank = 0;
-    if(array_key_exists($type_id, $ranks)) {
-      $rank = count($ranks[$type_id]);
-    }
-
-    // skip any properties that the user requested to delete through a previous
-    // AHAH callback or through the current AHAH callback
-    if (array_key_exists("$type_id-$rank", $d_removed)) {
-      continue;
-    }
-    if (array_key_exists('triggering_element', $form_state) and 
-        $form_state['triggering_element']['#name'] == 'remove-' . $type_id . '-' . $rank) {
-      $d_removed["$type_id-$rank"] = 1;
-      continue;
-    }
-
-    $ranks[$type_id][$rank]['name']  = $prop->name;
-    $ranks[$type_id][$rank]['id']    = $type_id;
-    $ranks[$type_id][$rank]['value'] = $prop->value;
-    $ranks[$type_id][$rank]['definition']  = $prop->definition;
-    $num_properties++;
-    $rows = 1;
-
-    $form['properties']['table'][$type_id][$rank]["prop_id-$type_id-$rank"] = array(
-      '#markup'        => $prop->name,
-    );
-    $form['properties']['table'][$type_id][$rank]["prop_value-$type_id-$rank"] = array(
-      '#type'          => 'textarea',
-      '#default_value' => $prop->value,
-      '#cols'          => 50,
-      '#rows'          => $rows,
-      '#description'   => $prop->definition,
-    );
-
-    $form['properties']['table'][$type_id][$rank]["remove-$type_id-$rank"] = array(
-      '#type'         => 'button',
-      '#value'        => t('Remove'),
-      '#name'         => "remove-$type_id-$rank",
-      '#ajax' => array(
-        'callback' => "tripal_analysis_property_ajax_update",
-        'wrapper'  => 'tripal-analysis-edit-properties-table',
-        'effect'   => 'fade',
-        'event'    => 'mousedown',
-        'method'   => 'replace',
-        'prevent'  => 'click'
-      ),
-      // When this button is clicked, the form will be validated and submitted.
-      // Therefore, we set custom submit and validate functions to override the
-      // default form submit.  In the validate function we set the form_state
-      // to rebuild the form so the submit function never actually gets called,
-      // but we need it or Drupal will run the default validate anyway.
-      // we also set #limit_validation_errors to empty so fields that
-      // are required that don't have values won't generate warnings.
-      '#submit'   => array('chado_analysis_node_form_props_button_submit'),
-      '#validate' => array('chado_analysis_node_form_props_button_validate'),
-      '#limit_validation_errors' => array(),
-    );
-  }
-  return $num_properties;
-}
-
 /**
  * Validates the user input before creating an analysis node
  *
@@ -667,114 +315,4 @@ function tripal_analysis_validate($node, &$form_state) {
       }
     }
   }
-}
-
-
-/*
- *
- */
-function tripal_analysis_theme_node_form_properties($form) {
-  $rows = array();
-
-  if (array_key_exists('properties', $form)) {
-
-    // first add in the properties derived from the analysisprop table
-    // the array tree for these properties looks like this:
-    // $form['properties']['table'][$type_id][$rank]["prop_id-$type_id-$rank"]
-    foreach ($form['properties']['table'] as $type_id => $elements) {
-      // there are other fields in the properties array so we only
-      // want the numeric ones those are our type_id
-      if (is_numeric($type_id)) {
-        foreach ($elements as $rank => $element) {
-          if (is_numeric($rank)) {
-            $rows[] = array(
-              drupal_render($element["prop_id-$type_id-$rank"]),
-              drupal_render($element["prop_value-$type_id-$rank"]),
-              drupal_render($element["remove-$type_id-$rank"]),
-            );
-          }
-        }
-      }
-    }
-
-    // second, add in any new properties added by the user through AHAH callbacks
-    // the array tree for these properties looks like this:
-    // $form['properties']['table']['new'][$type_id][$rank]["new_id-$new_id-$rank"]
-    foreach ($form['properties']['table']['new'] as $type_id => $elements) {
-      if (is_numeric($type_id)) {
-        foreach ($elements as $rank => $element) {
-          if (is_numeric($rank)) {
-            $rows[] = array(
-              drupal_render($element["new_id-$type_id-$rank"]),
-              drupal_render($element["new_value-$type_id-$rank"]),
-              drupal_render($element["remove-$type_id-$rank"]),
-            );
-          }
-        }
-      }
-    }
-
-    // finally add in a set of blank field for adding a new property
-    $rows[] = array(
-      drupal_render($form['properties']['table']['new']['new_id']),
-      array(
-        'data' => drupal_render($form['properties']['table']['new']['new_value']),
-        'width' => '60%',
-      ),
-      drupal_render($form['properties']['table']['new']['add']),
-    );
-  }
-  $headers = array('Property Type', 'Value', 'Actions');
-  $table = array(
-    'header' => $headers,
-    'rows' => $rows,
-    'attributes' => array(),
-    'sticky' => TRUE,
-    'caption' => '',
-    'colgroups' => array(),
-    'empty' => '',
-  );
-  
-  return theme_table($table); 
-}
-
-/**
- * Form AJAX callback for adding a blank property row
- * 
- * We only want to return the properties as that's all we'll replace with this callback
- */
-function tripal_analysis_property_ajax_update($form, $form_state) {
-  $properties_html = tripal_analysis_theme_node_form_properties($form); 
-  $form['properties']['table'] = array(
-    '#markup' => $properties_html,
-    '#prefix' => '<div id="tripal-analysis-edit-properties-table">',
-    '#suffix' => '</div>',
-  );
-  return $form['properties']['table'];
-}
-/**
- * Form AJAX callback for updating a property description. This 
- * function only gets called when the property drop down is changed
- * on the bottom (empty) row of properties
- */
-function tripal_analysis_property_get_description($form, $form_state) {
-  return $form['properties']['table']['new']["new_value"];
-}
-
-/**
- * We need to theme the analysis form so that the properties fields look good
- */
-function theme_chado_analysis_form($variables) {
-  $form = $variables['form'];
-
-  $properties_table = tripal_analysis_theme_node_form_properties($form);
-  $markup = $properties_table;
-
-  $form['properties']['table'] = array(
-    '#markup' => $markup,
-    '#prefix' => '<div id="tripal-analysis-edit-properties-table">',
-    '#suffix' => '</div>',
-  );
-  $form['buttons']['#weight'] = 50; 
-  return drupal_render_children($form);
 }

tripal_analysis/theme/tripal_analysis/tripal_analysis_properties.tpl.php

@@ -3,14 +3,7 @@
 // get the analysis object and expand it to include the records from the analysisprop table
 $analysis = $variables['node']->analysis;
 $analysis = tripal_core_expand_chado_vars($analysis,'table', 'analysisprop', array('return_array' => 1));
-$analysisprops = $analysis->analysisprop;
-
-// put the properties in an array for easier access
-$properties = array();
-foreach ($analysisprops as $property) {
-  $property = tripal_core_expand_chado_vars($property,'field','analysisprop.value');
-  $properties[] = $property;
-}
+$properties = $analysis->analysisprop;
 
 if (count($properties) > 0) { ?>
   <div id="tripal_analysis-properties-box" class="tripal_analysis-info-box tripal-info-box">

tripal_analysis/tripal_analysis.module

@@ -186,11 +186,6 @@ function tripal_analysis_theme($existing, $type, $theme, $path) {
       'variables' =>  array('node' => NULL),
       'path' => "$path/theme/tripal_analysis",
     ),
-    
-    // form theme
-    'chado_analysis_form' => array(
-      'render element' => 'form',
-    )
 
   );
 
@@ -361,6 +356,20 @@ function chado_analysis_insert($node) {
       return;
     }
     $analysis_id = $analysis['analysis_id'];
+    
+    // now add in the properties
+    $properties = tripal_core_properties_form_retreive($node, 'analysis_property');
+    foreach ($properties as $property => $elements) {
+      foreach ($elements as $rank => $value) {
+    
+        $status = tripal_analysis_insert_property($analysis_id, $property, $value, FALSE, 'analysis_property');
+        if (!$status) {
+          drupal_set_message("Error cannot add property: $property", "error");
+          watchdog('t_analysis', "Error cannot add property: %prop",
+          array('%property' => $property), WATCHDOG_ERROR);
+        }
+      }
+    }
   }
   else {
     $analysis_id = $node->analysis_id;
@@ -381,60 +390,6 @@ function chado_analysis_insert($node) {
   // use by other analysis modules that may be using this function
   $node->analysis = $analysis;
   $node->analysis_id = $analysis_id; // we need to set this for children
-
-  // now add the properties
-  $properties = array(); // stores all of the properties we need to add
-
-  // get the list of properties for easy lookup (without doing lots of database queries
-  $properties_list = array();
-  $sql = "
-      SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
-      FROM  {cvterm} CVT
-        INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
-      WHERE
-        CV.name = 'analysis_property' AND
-        NOT CVT.is_obsolete = 1
-      ORDER BY CVT.name ASC
-  ";
-  $prop_types = chado_query($sql);
-  while ($prop = $prop_types->fetchObject()) {
-    $properties_list[$prop->cvterm_id] = $prop->name;
-  }
-
-  // get the properties that should be added. Properties are in one of two forms:
-  //  1) prop_value-[type id]-[index]
-  //  2) new_value-[type id]-[index]
-  //  3) new_id, new_value
-
-  foreach ($node as $name => $value) {
-    if (preg_match('/^new_value-(\d+)-(\d+)/', $name, $matches)) {
-      $type_id = $matches[1];
-      $index = $matches[2];
-      $name = $properties_list[$type_id];
-      $properties[$name][$index] = trim($value);
-    }
-  }
-  if ($node->new_id and $node->new_value) {
-    $type_id = $node->new_id;
-    $name = $properties_list[$type_id];
-    $index = 0;
-    if (array_key_exists($name, $properties)) {
-      $index = count($properties[$name]);
-    }
-    $properties[$name][$index] = trim($node->new_value);
-  }
-  
-  // now add in the properties
-  foreach ($properties as $property => $elements) {
-    foreach ($elements as $rank => $value) {
-      $status = tripal_analysis_insert_property($analysis_id, $property, $value, FALSE, 'analysis_property');
-      if (!$status) {
-          drupal_set_message("Error cannot add property: $property", "error");
-          watchdog('t_analysis', "Error cannot add property: %prop",
-            array('%property' => $property), WATCHDOG_ERROR);
-      }
-    }
-  }
 }
 
 /**
@@ -517,67 +472,17 @@ function chado_analysis_update($node) {
   // now update the properties
   $properties = array(); // stores all of the properties we need to add
   
-  // get the list of properties for easy lookup (without doing lots of database queries
-  $properties_list = array();
-  $sql = "
-    SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
-    FROM  {cvterm} CVT
-      INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
-    WHERE CV.name = 'analysis_property' AND NOT CVT.is_obsolete = 1
-    ORDER BY CVT.name ASC
-  ";
-  $prop_types = chado_query($sql);
-  while ($prop = $prop_types->fetchObject()) {
-    $properties_list[$prop->cvterm_id] = $prop->name;
-  }
-
-  // get the properties that should be added. Properties are in one of three forms:
-  //  1) prop_value-[type id]-[index]
-  //  2) new_value-[type id]-[index]
-  //  3) new_id, new_value
-  foreach ($node as $key => $value) {
-    if (preg_match('/^prop_value-(\d+)-(\d+)/', $key, $matches)) {
-      $type_id = $matches[1];
-      $index = $matches[2];
-      $name = $properties_list[$type_id];
-      $properties[$name][$index] = trim($value);
-    }
-    if (preg_match('/^new_value-(\d+)-(\d+)/', $key, $matches)) {
-      $type_id = $matches[1];
-      $index = $matches[2];
-      $name = $properties_list[$type_id];
-      $properties[$name][$index] = trim($value);
-    }
-  }
-  if ($node->new_id and $node->new_value) {
-    $type_id = $node->new_id;
-    $name = $properties_list[$type_id];
-    $index = count($properties[$name]);
-    $properties[$name][$index] = trim($node->new_value);
-  }
-
   // now add in the properties by first removing any the analysis
   // already has and adding the ones we have
-  $sql = "
-    DELETE FROM {analysisprop} WHERE analysis_id = :analysis_id AND type_id IN (
-      SELECT CVT.cvterm_id
-      FROM  {cvterm} CVT
-        INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
-      WHERE CV.name = 'analysis_property')
-  ";
-  $success = chado_query($sql, array(':analysis_id' => $analysis_id));
-  if (!$success) {
-    drupal_set_message("Cannot update analysis properties", "error");
-    watchdog('t_analysis', "Cannot update analysis properties.", array(), WATCHDOG_ERROR);
-    return;
-  }
+  tripal_core_chado_delete('analysisprop', array('analysis_id' => $analysis_id));
+  $properties = tripal_core_properties_form_retreive($node, 'analysis_property');
   foreach ($properties as $property => $elements) {
     foreach ($elements as $rank => $value) {
       $status = tripal_analysis_insert_property($analysis_id, $property, $value, FALSE, 'analysis_property');
       if (!$status) {
         drupal_set_message("Error cannot add property: '$property'", "error");
         watchdog('t_analysis', "Error cannot add property: '%prop'",
-          array('%prop' => $property), WATCHDOG_ERROR);
+        array('%prop' => $property), WATCHDOG_ERROR);
       }
     }
   }

tripal_contact/theme/tripal_contact/tripal_contact_properties.tpl.php

@@ -5,14 +5,16 @@ $contact = $variables['node']->contact;
 $contact = tripal_core_expand_chado_vars($contact,'table', 'contactprop', array('return_array' => 1));
 $contactprops = $contact->contactprop;
 
-// put the properties in an array for easier access
+// put the properties in an array so we can remove the contact_description property
 $properties = array();
-foreach ($contactprops as $property) {
-  // we want to keep all properties but the contact_description as that
-  // property is shown on the base template page.
-  if($property->type_id->name != 'contact_description') {
-    $property = tripal_core_expand_chado_vars($property,'field','contactprop.value');
-    $properties[] = $property;
+if ($contactprops) {
+  foreach ($contactprops as $property) {
+    // we want to keep all properties but the contact_description as that
+    // property is shown on the base template page.
+    if($property->type_id->name != 'contact_description') {
+      $property = tripal_core_expand_chado_vars($property,'field','contactprop.value');
+      $properties[] = $property;
+    }
   }
 }
 

tripal_core/api/tripal_core_chado.api.inc

@@ -1482,7 +1482,7 @@ function tripal_core_generate_chado_var($table, $values, $base_options = array()
 
   // Expandable fields without value needed for criteria--------------------------------------------
   $all->expandable_fields = array();
-  if (array_key_exists('referring_tables', $table_desc)) {
+  if (array_key_exists('referring_tables', $table_desc) and $table_desc['referring_tables']) {
     $all->expandable_tables = $table_desc['referring_tables'];
   }
   else {
@@ -1620,21 +1620,24 @@ function tripal_core_generate_chado_var($table, $values, $base_options = array()
             // add the foreign record to the current object in a nested manner
             $object->{$foreign_key} = $foreign_object;
             // Flatten expandable_x arrays so only in the bottom object
-            if (property_exists($object->{$foreign_key}, 'expandable_fields') and is_array($object->{$foreign_key}->expandable_fields)) {
+            if (property_exists($object->{$foreign_key}, 'expandable_fields') and 
+                is_array($object->{$foreign_key}->expandable_fields)) {
               $object->expandable_fields = array_merge(
                 $object->expandable_fields,
                 $object->{$foreign_key}->expandable_fields
               );
               unset($object->{$foreign_key}->expandable_fields);
             }
-            if (property_exists($object->{$foreign_key}, 'expandable_tables') and is_array($object->{$foreign_key}->expandable_tables)) {
+            if (property_exists($object->{$foreign_key}, 'expandable_tables') and 
+                is_array($object->{$foreign_key}->expandable_tables)) {
               $object->expandable_tables = array_merge(
                 $object->expandable_tables,
                 $object->{$foreign_key}->expandable_tables
               );
               unset($object->{$foreign_key}->expandable_tables);
             }
-            if (property_exists($object->{$foreign_key}, 'expandable_nodes') and is_array($object->{$foreign_key}->expandable_nodes)) {
+            if (property_exists($object->{$foreign_key}, 'expandable_nodes') and 
+                is_array($object->{$foreign_key}->expandable_nodes)) {
               $object->expandable_nodes = array_merge(
                 $object->expandable_nodes,
                 $object->{$foreign_key}->expandable_nodes

tripal_core/api/tripal_core_properties.api.inc

@@ -116,8 +116,8 @@ $cv_name, $value, $update_if_present = 0) {
   $options = array();
   $term = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
   if (!$term or count($term) == 0) {
-    watchdog('tripal_core', "Cannot find property '%prop_name'.",
-    array('%prop_name' => $property), WATCHDOG_ERROR);
+    watchdog('tripal_core', "Cannot find property '%prop_name' in vocabulary '%cvname'.",
+    array('%prop_name' => $property, '%cvname' => $cv_name), WATCHDOG_ERROR);
     return FALSE;
   }