API: Fixed property api calls

tripal_feature/api/tripal_feature.DEPRECATED.inc

@@ -23,7 +23,24 @@ function tripal_feature_analysis_get_property($analysis_id = NULL, $feature_id =
     )
   );
 
-  return FALSE;
+  // check that the incoming arguments are correct
+  if (($analysis_id and !$feature_id) or
+    (!$analysis_id and $feature_id)) {
+      tripal_report_error('tripal_feature', TRIPAL_WARNING,
+      'tripal_feature_analysis_get_property: Both an analysis ID and feature ID should be specified',
+      array());
+  }
+
+  // get the analysisfeature_id if one is not provided
+  if (!$analysisfeature_id) {
+    $columns = array('analysisfeature_id');
+    $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
+    $result = chado_select_record('analysisfeature', $columns, $values);
+    $analysisfeature_id = $result[0]->analysisfeature_id;
+  }
+
+  // get the property.
+  return chado_get_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
 }
 
 /**
@@ -45,7 +62,26 @@ function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_i
     )
   );
 
-  return FALSE;
+    // check that the incoming arguments are correct
+  if (($analysis_id and !$feature_id) or
+      (!$analysis_id and $feature_id)) {
+    tripal_report_error('tripal_feature', TRIPAL_WARNING,
+      'tripal_feature_analysis_insert_property: Both an analysis ID and feature ID should be specified',
+      array());
+  }
+
+  // get the analysisfeature_id if one is not provided
+  if (!$analysisfeature_id) {
+    $columns = array('analysisfeature_id');
+    $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
+    $result = chado_select_record('analysisfeature', $columns, $values);
+    $analysisfeature_id = $result[0]->analysisfeature_id;
+  }
+
+  // insert the property.
+  return chado_insert_property('analysisfeature', $analysisfeature_id,
+    $property, $cv_name, $value, $update_if_present);
+
 }
 
 /**
@@ -67,7 +103,24 @@ function tripal_feature_analysis_update_property($analysis_id = NULL, $feature_i
     )
   );
 
-  return FALSE;
+  // check that the incoming arguments are correct
+  if (($analysis_id and !$feature_id) or
+    (!$analysis_id and $feature_id)) {
+      tripal_report_error('tripal_feature', TRIPAL_WARNING,
+      'tripal_feature_analysis_update_property: Both an analysis ID and feature ID should be specified',
+      array());
+  }
+
+  // get the analysisfeature_id if one is not provided
+  if (!$analysisfeature_id) {
+    $columns = array('analysisfeature_id');
+    $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
+    $result = chado_select_record('analysisfeature', $columns, $values);
+    $analysisfeature_id = $result[0]->analysisfeature_id;
+  }
+
+  // update the property.
+  return chado_update_property('analysisfeature', $analysisfeature_id, $property, $cv_name, $value, $insert_if_missing);
 }
 
 /**
@@ -89,7 +142,8 @@ function tripal_feature_analysis_update_property_by_id($analysisfeatureprop_id,
     )
   );
 
-  return FALSE;
+  // update the property.
+  return chado_update_property('analysisfeature', NULL, $property, $cv_name, $value, FALSE, $analysisfeatureprop_id);
 }
 
 /**
@@ -111,15 +165,33 @@ function tripal_feature_analysis_delete_property($analysis_id = NULL, $feature_i
     )
   );
 
-  return FALSE;
+  // check that the incoming arguments are correct
+  if (($analysis_id and !$feature_id) or
+    (!$analysis_id and $feature_id)) {
+      tripal_report_error('tripal_feature', TRIPAL_WARNING,
+      'tripal_feature_analysis_delete_property: Both an analysis ID and feature ID should be specified',
+        array());
+  }
+
+  // get the analysisfeature_id if one is not provided
+  if (!$analysisfeature_id) {
+    $columns = array('analysisfeature_id');
+    $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
+    $result = chado_select_record('analysisfeature', $columns, $values);
+    $analysisfeature_id = $result[0]->analysisfeature_id;
+  }
+
+  // get the property.
+  return chado_delete_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
+
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by chado_delete_property().
+ * This function has been replaced by chado_delete_record().
  *
- * @see chado_delete_property().
+ * @see chado_delete_record().
  */
 function tripal_feature_analysis_delete_property_by_id($analysisfeatureprop_id) {
 
@@ -133,7 +205,12 @@ function tripal_feature_analysis_delete_property_by_id($analysisfeatureprop_id)
     )
   );
 
-  return FALSE;
+  // construct the array that will match the exact record to update
+  $match = array(
+    'analysisfeatureprop_id' => $analysisfeatureprop_id,
+  );
+
+  return chado_delete_record('analysisfeatureprop', $match);
 }
 
 /**
@@ -155,7 +232,7 @@ function tripal_feature_get_property($feature_id, $property, $cv_name='tripal')
     )
   );
 
-  return FALSE;
+  return chado_get_property('feature', $feature_id, $property, $cv_name);
 }
 
 /**
@@ -177,7 +254,8 @@ function tripal_feature_insert_property($feature_id, $property, $value, $update_
     )
   );
 
-  return FALSE;
+  return chado_insert_property('feature', $feature_id, $property,
+    $cv_name, $value, $update_if_present);
 }
 
 /**
@@ -199,7 +277,7 @@ function tripal_feature_update_property($feature_id, $property, $value, $insert_
     )
   );
 
-  return FALSE;
+  return chado_update_property('feature', $feature_id, $property, $cv_name, $value, $insert_if_missing);
 }
 
 /**
@@ -221,7 +299,7 @@ function tripal_feature_update_property_by_id($featureprop_id, $property, $value
     )
   );
 
-  return FALSE;
+  return chado_update_property('feature', NULL, $property, $cv_name, $value, FALSE, $featureprop_id);
 }
 
 /**
@@ -243,15 +321,15 @@ function tripal_feature_delete_property($feature_id, $property, $cv_name='tripal
     )
   );
 
-  return FALSE;
+  return chado_delete_property('feature', $feature_id, $property, $cv_name);
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by chado_delete_property().
+ * This function has been replaced by chado_delete_record().
  *
- * @see chado_delete_property().
+ * @see chado_delete_record().
  */
 function tripal_feature_delete_property_by_id($featureprop_id) {
 
@@ -265,7 +343,12 @@ function tripal_feature_delete_property_by_id($featureprop_id) {
     )
   );
 
-  return FALSE;
+  // construct the array that will match the exact record to update
+  $match = array(
+    'featureprop_id' => $featureprop_id,
+  );
+
+  return chado_delete_record('featureprop', $match);
 }
 
 /**

tripal_pub/api/tripal_pub.DEPRECATED.inc

@@ -309,7 +309,7 @@ function tripal_pub_get_property($pub_id, $property) {
     )
   );
 
-  return FALSE;
+  return chado_get_property('pub', $pub_id, $property, 'tripal_pub');
 }
 
 /**
@@ -331,7 +331,7 @@ function tripal_pub_insert_property($pub_id, $property, $value, $update_if_prese
     )
   );
 
-  return FALSE;
+  return chado_insert_property('pub', $pub_id, $property, 'tripal_pub', $value, $update_if_present);
 }
 
 /**
@@ -353,7 +353,7 @@ function tripal_pub_update_property($pub_id, $property, $value, $insert_if_missi
     )
   );
 
-  return FALSE;
+  return chado_update_property('pub', $pub_id, $property, 'tripal_pub', $value, $insert_if_missing);
 }
 
 /**
@@ -375,7 +375,7 @@ function tripal_pub_delete_property($pub_id, $property) {
     )
   );
 
-  return FALSE;
+  return chado_delete_property('pub', $pub_id, $property, 'tripal_pub');
 }
 
 /**