Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x

tripal_contact/api/tripal_contact.DEPRECATED.inc

@@ -0,0 +1,115 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal contact api
+ */
+
+/**
+ * @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+ * This function has been replaced by chado_get_property().
+ *
+ * @see chado_get_property().
+ */
+function tripal_contact_get_property($contact_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_contact_get_property',
+      '%new_function' => 'chado_get_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_property().
+ *
+ * @see chado_insert_property().
+ */
+function tripal_contact_insert_property($contact_id, $property, $value, $update_if_present = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_contact_insert_property',
+      '%new_function' => 'chado_insert_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_contact_update_property($contact_id, $property, $value, $insert_if_missing = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_contact_update_property',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_contact_delete_property($contact_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_contact_delete_property',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_contact().
+ *
+ * @see chado_insert_contact().
+ */
+function tripal_contact_add_contact($name, $description, $type, $properties) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_contact_add_contact',
+      '%new_function' => 'chado_insert_contact'
+    )
+  );
+
+  return FALSE;
+}

tripal_contact/tripal_contact.module

@@ -14,12 +14,13 @@
  * @}
  */
 
-require 'api/tripal_contact.api.inc';
+require_once 'api/tripal_contact.api.inc';
+// require_once 'api/tripal_contact.DEPRECATED.inc';
 
-require 'theme/tripal_contact.theme.inc';
+require_once 'theme/tripal_contact.theme.inc';
 
-require 'includes/tripal_contact.admin.inc';
-require 'includes/tripal_contact.chado_node.inc';
+require_once 'includes/tripal_contact.admin.inc';
+require_once 'includes/tripal_contact.chado_node.inc';
 
 /**
  * Implements hook_views_api().

tripal_cv/api/tripal_cv.DEPRECATED.inc

@@ -0,0 +1,335 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal cv api
+ */
+
+/**
+ * @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_get_cv().
+ *
+ * @see chado_get_cv().
+ */
+function tripal_cv_get_cv($select_values) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cv',
+      '%new_function' => 'chado_get_cv'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_cv().
+ *
+ * @see chado_get_cv().
+ */
+function tripal_cv_get_cv_by_name($name) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cv_by_name',
+      '%new_function' => 'chado_get_cv'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_get_cv().
+ *
+ * @see chado_get_cv().
+ */
+function tripal_cv_get_cv_by_id($cv_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cv_by_id',
+      '%new_function' => 'chado_get_cv'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_cv().
+ *
+ * @see chado_get_cv().
+ */
+function tripal_cv_get_cv_id($cv_name) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cv_id',
+      '%new_function' => 'chado_get_cv'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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 cv_get_select_options().
+ *
+ * @see cv_get_select_options().
+ */
+function tripal_cv_get_cv_options() {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cv_options',
+      '%new_function' => 'cv_get_select_options'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_get_cvterm().
+ *
+ * @see chado_get_cvterm().
+ */
+function tripal_cv_get_cvterm_by_id($cvterm_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cvterm_by_id',
+      '%new_function' => 'chado_get_cvterm'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_cvterm().
+ *
+ * @see chado_get_cvterm().
+ */
+function tripal_cv_get_cvterm_by_name($name, $cv_id = NULL, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cvterm_by_name',
+      '%new_function' => 'chado_get_cvterm'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_cvterm().
+ *
+ * @see chado_get_cvterm().
+ */
+function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cvterm_by_synonym',
+      '%new_function' => 'chado_get_cvterm'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by cvterm_get_select_options().
+ *
+ * @see cvterm_get_select_options().
+ */
+function tripal_cv_get_cvterm_options($cv_id = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_get_cvterm_options',
+      '%new_function' => 'cvterm_get_select_options'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_update_cvtermpath().
+ *
+ * @see chado_update_cvtermpath().
+ */
+function tripal_cv_update_cvtermpath($cvid, $job_id = NULL) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_update_cvtermpath',
+      '%new_function' => 'chado_update_cvtermpath'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_cv().
+ *
+ * @see chado_insert_cv().
+ */
+function tripal_cv_add_cv($name, $definition) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_add_cv',
+      '%new_function' => 'chado_insert_cv'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_cvterm().
+ *
+ * @see chado_insert_cvterm().
+ */
+function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship = 0, $update = 1, $dbname = 'internal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_add_cvterm',
+      '%new_function' => 'chado_insert_cvterm'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by tripal_submit_obo_job().
+ *
+ * @see tripal_submit_obo_job().
+ */
+function tripal_cv_submit_obo_job($obo_id = NULL, $obo_name = NULL, $obo_url = NULL, $obo_file = NULL) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_submit_obo_job',
+      '%new_function' => 'tripal_submit_obo_job'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_obo().
+ *
+ * @see chado_insert_obo().
+ */
+function tripal_cv_add_obo_ref($name, $path) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_add_obo_ref',
+      '%new_function' => 'chado_insert_obo'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_cvterm_autocomplete().
+ *
+ * @see chado_cvterm_autocomplete().
+ */
+function tripal_cv_cvterm_name_autocomplete($cv_id, $string = '') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_cv_cvterm_name_autocomplete',
+      '%new_function' => 'chado_cvterm_autocomplete'
+    )
+  );
+
+  return FALSE;
+}

tripal_cv/tripal_cv.module

@@ -16,6 +16,7 @@
 
 require_once 'api/tripal_cv.api.inc';
 require_once 'api/tripal_cv.schema.api.inc';
+//require_once 'apitripal_cv.DEPRECATED.inc';
 
 require_once 'includes/tripal_cv.admin.inc';
 require_once 'includes/tripal_cv.charts.inc';

tripal_db/api/tripal_db.DEPRECATED.inc

@@ -0,0 +1,203 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal db api
+ */
+
+/**
+ * @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_get_db().
+ *
+ * @see chado_get_db().
+ */
+function tripal_db_get_db($select_values) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_get_db',
+      '%new_function' => 'chado_get_db'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_db().
+ *
+ * @see chado_get_db().
+ */
+function tripal_db_get_db_by_db_id($db_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_get_db_by_db_id',
+      '%new_function' => 'chado_get_db'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_get_db().
+ *
+ * @see chado_get_db().
+ */
+function tripal_db_get_db_by_name($name) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_get_db_by_name',
+      '%new_function' => 'chado_get_db'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by db_get_select_options().
+ *
+ * @see db_get_select_options().
+ */
+function tripal_db_get_db_options() {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_get_db_options',
+      '%new_function' => 'db_get_select_options'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_db().
+ *
+ * @see chado_get_dbxref().
+ */
+function tripal_db_get_dbxref($select_values) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_get_dbxref',
+      '%new_function' => 'chado_get_dbxref'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_get_db().
+ *
+ * @see chado_get_dbxref().
+ */
+function tripal_db_get_dbxref_by_accession($accession, $db_id=0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_get_dbxref_by_accession',
+      '%new_function' => 'chado_get_dbxref'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_db().
+ *
+ * @see chado_insert_db().
+ */
+function tripal_db_add_db($dbname, $description = '', $url = '', $urlprefix = '', $update = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_add_db',
+      '%new_function' => 'chado_insert_db'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_dbxref().
+ *
+ * @see chado_insert_dbxref().
+ */
+function tripal_db_add_dbxref($db_id, $accession, $version = '', $description = '') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_add_dbxref',
+      '%new_function' => 'chado_insert_dbxref'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_associate_dbxref().
+ *
+ * @see chado_associate_dbxref().
+ */
+function tripal_db_add_dbxref_link($linking_table, $dbxref_id, $foreignkey_name, $foreignkey_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_db_add_dbxref_link',
+      '%new_function' => 'chado_associate_dbxref'
+    )
+  );
+
+  return FALSE;
+}

tripal_db/tripal_db.module

@@ -5,6 +5,8 @@
  */
 
 require_once 'api/tripal_db.api.inc';
+//require_once 'api/tripal_db.DEPRECATED.inc';
+
 require_once 'includes/tripal_db.admin.inc';
 
 /**

tripal_feature/api/tripal_feature.DEPRECATED.inc

@@ -0,0 +1,379 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal feature api
+ */
+
+/**
+ * @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_get_property().
+ *
+ * @see chado_get_property().
+ */
+function tripal_feature_analysis_get_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_analysis_get_property',
+      '%new_function' => 'chado_get_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_property().
+ *
+ * @see chado_insert_property().
+ */
+function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $value, $update_if_present = 0, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_analysis_insert_property',
+      '%new_function' => 'chado_insert_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_feature_analysis_update_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $value, $insert_if_missing = 0, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_analysis_update_property',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_feature_analysis_update_property_by_id($analysisfeatureprop_id, $property, $value, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_analysis_update_property_by_id',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_feature_analysis_delete_property($analysis_id = NULL, $feature_id = NUll, $analysisfeature_id = NULL, $property, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_analysis_delete_property',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_feature_analysis_delete_property_by_id($analysisfeatureprop_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_analysis_delete_property_by_id',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_get_property().
+ *
+ * @see chado_get_property().
+ */
+function tripal_feature_get_property($feature_id, $property, $cv_name='tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_get_property',
+      '%new_function' => 'chado_get_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_property().
+ *
+ * @see chado_insert_property().
+ */
+function tripal_feature_insert_property($feature_id, $property, $value, $update_if_present = 0, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_insert_property',
+      '%new_function' => 'chado_insert_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_feature_update_property($feature_id, $property, $value, $insert_if_missing = 0, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_update_property',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_feature_update_property_by_id($featureprop_id, $property, $value, $cv_name = 'tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_update_property_by_id',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_feature_delete_property($feature_id, $property, $cv_name='tripal') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_delete_property',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_feature_delete_property_by_id($featureprop_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_delete_property_by_id',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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 feature_sequence_reverse_complement().
+ *
+ * @see feature_sequence_reverse_complement().
+ */
+function tripal_feature_reverse_complement($sequence) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_reverse_complement',
+      '%new_function' => 'feature_sequence_reverse_complement'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by feature_sequence_get_formatted().
+ *
+ * @see feature_sequence_get_formatted().
+ */
+function tripal_feature_get_formatted_sequence($feature_id, $feature_name, $num_bases_per_line, $derive_from_parent, $aggregate, $output_format, $upstream, $downstream, $sub_features = array(), $relationship = '', $rel_part = '') {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_get_formatted_sequence',
+      '%new_function' => 'feature_sequence_get_formatted'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_associate_dbxref().
+ *
+ * @see chado_associate_dbxref().
+ */
+function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_add_dbxref',
+      '%new_function' => 'chado_associate_dbxref'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_associate_cvterm().
+ *
+ * @see chado_associate_cvterm().
+ */
+function tripal_feature_add_cvterm($feature_id, $cvname, $cvterm) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_add_cvterm',
+      '%new_function' => 'chado_associate_cvterm'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by feature_sequence_get_fasta().
+ *
+ * @see feature_sequence_get_fasta().
+ */
+function tripal_feature_return_fasta($feature, $desc) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_feature_return_fasta',
+      '%new_function' => 'feature_sequence_get_fasta'
+    )
+  );
+
+  return FALSE;
+}

tripal_feature/tripal_feature.module

@@ -14,6 +14,7 @@
 
 require_once 'api/tripal_feature.api.inc';
 require_once 'api/tripal_feature.schema.api.inc';
+//require_once 'api/tripal_feature.DEPRECATED.inc';
 
 require_once 'theme/tripal_feature.theme.inc';
 

tripal_featuremap/api/tripal_featuremap.DEPRECATED.inc

@@ -0,0 +1,115 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal featuremap api
+ */
+
+/**
+ * @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_get_property().
+ *
+ * @see chado_get_property().
+ */
+function tripal_featuremap_get_property($featuremap_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_featuremap_get_property',
+      '%new_function' => 'chado_get_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_property().
+ *
+ * @see chado_insert_property().
+ */
+function tripal_featuremap_insert_property($featuremap_id, $property, $value, $update_if_present = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_featuremap_insert_property',
+      '%new_function' => 'chado_insert_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_featuremap_update_property($featuremap_id, $property, $value, $insert_if_missing = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_featuremap_update_property',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_featuremap_delete_property($featuremap_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_featuremap_delete_property',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_associate_dbxref().
+ *
+ * @see chado_associate_dbxref().
+ */
+function tripal_featuremap_add_featuremap_dbxref($featuremap_id, $featuremap_dbxref) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_featuremap_add_featuremap_dbxref',
+      '%new_function' => 'chado_associate_dbxref'
+    )
+  );
+
+  return FALSE;
+}

tripal_featuremap/tripal_featuremap.module

@@ -12,12 +12,13 @@
  * @}
  */
 
-require 'api/tripal_featuremap.api.inc';
+require_once 'api/tripal_featuremap.api.inc';
+//require_once 'api/tripal_featuremap.DEPRECATED.inc';
 
-require 'theme/tripal_featuremap.theme.inc';
+require_once 'theme/tripal_featuremap.theme.inc';
 
-require 'includes/tripal_featuremap.admin.inc';
-require 'includes/tripal_featuremap.chado_node.inc';
+require_once 'includes/tripal_featuremap.admin.inc';
+require_once 'includes/tripal_featuremap.chado_node.inc';
 
 /**
  * Implements hook_help().

tripal_genetic/tripal_genetic.module

@@ -12,12 +12,12 @@
  * @}
  */
 
-require 'api/tripal_genetic.api.inc';
+require_once 'api/tripal_genetic.api.inc';
 
-require 'theme/tripal_genetic.theme.inc';
+require_once 'theme/tripal_genetic.theme.inc';
 
-require 'includes/tripal_genetic.schema.inc';
-require 'includes/tripal_genetic.admin.inc';
+require_once 'includes/tripal_genetic.schema.inc';
+require_once 'includes/tripal_genetic.admin.inc';
 
 /**
  * Implements hook_permission().

tripal_library/api/tripal_library.DEPRECATED.inc

@@ -0,0 +1,93 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal library api
+ */
+
+/**
+ * @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_get_property().
+ *
+ * @see chado_get_property().
+ */
+function tripal_library_get_property($library_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_library_get_property',
+      '%new_function' => 'chado_get_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_property().
+ *
+ * @see chado_insert_property().
+ */
+function tripal_library_insert_property($library_id, $property, $value, $update_if_present = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_library_insert_property',
+      '%new_function' => 'chado_insert_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_library_update_property($library_id, $property, $value, $insert_if_missing = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_library_update_property',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_library_delete_property($library_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_library_delete_property',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}

tripal_library/tripal_library.module

@@ -12,12 +12,13 @@
  * @}
  */
 
-require 'api/tripal_library.api.inc';
+require_once 'api/tripal_library.api.inc';
+//require_once 'api/tripal_library.DEPRECATED.inc';
 
-require 'theme/tripal_library.theme.inc';
+require_once 'theme/tripal_library.theme.inc';
 
-require 'includes/tripal_library.admin.inc';
-require 'includes/tripal_library.chado_node.inc';
+require_once 'includes/tripal_library.admin.inc';
+require_once 'includes/tripal_library.chado_node.inc';
 
 /**
  * Implements hook_permission().

tripal_organism/api/tripal_organism.DEPRECATED.inc

@@ -0,0 +1,93 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal organism api
+ */
+
+/**
+ * @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_get_organism().
+ *
+ * @see chado_get_organism().
+ */
+function tripal_organism_get_organism_by_nid($nid) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_organism_get_organism_by_nid',
+      '%new_function' => 'chado_get_organism'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_organism().
+ *
+ * @see chado_get_organism().
+ */
+function tripal_organism_get_organism_by_organism_id($organism_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_organism_get_organism_by_organism_id',
+      '%new_function' => 'chado_get_organism'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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 organism_get_select_options().
+ *
+ * @see organism_get_select_options().
+ */
+function tripal_organism_get_synced() {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_organism_get_synced',
+      '%new_function' => 'organism_get_select_options'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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 organism_get_image().
+ *
+ * @see organism_get_image().
+ */
+function tripal_organism_get_image_url($organism, $nid = NULL) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_organism_get_image_url',
+      '%new_function' => 'organism_get_image'
+    )
+  );
+
+  return FALSE;
+}

tripal_organism/tripal_organism.module

@@ -5,6 +5,7 @@
  */
 
 require_once 'api/tripal_organism.api.inc';
+//require_once 'api/tripal_organism.DEPRECATED.inc';
 
 require_once 'includes/tripal_organism.admin.inc';
 require_once 'includes/tripal_organism.chado_node.inc';

tripal_project/api/tripal_project.DEPRECATED.inc

@@ -0,0 +1,93 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal project api
+ */
+
+/**
+ * @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_get_property().
+ *
+ * @see chado_get_property().
+ */
+function tripal_project_get_property($project_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_project_get_property',
+      '%new_function' => 'chado_get_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_property().
+ *
+ * @see chado_insert_property().
+ */
+function tripal_project_insert_property($project_id, $property, $value, $update_if_present = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_project_insert_property',
+      '%new_function' => 'chado_insert_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_project_update_property($project_id, $property, $value, $insert_if_missing = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_project_update_property',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_project_delete_property($project_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_project_delete_property',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}

tripal_project/tripal_project.module

@@ -4,12 +4,13 @@
  * Integrates the Chado Project tables with Drupal Nodes & Views
  */
 
-require 'api/tripal_project.api.inc';
+require_once 'api/tripal_project.api.inc';
+//require_once 'api/tripal_project.DEPRECATED.inc';
 
-require 'theme/tripal_project.theme.inc';
+require_once 'theme/tripal_project.theme.inc';
 
-require 'includes/tripal_project.admin.inc';
-require 'includes/tripal_project.chado_node.inc';
+require_once 'includes/tripal_project.admin.inc';
+require_once 'includes/tripal_project.chado_node.inc';
 
 /**
  * @defgroup tripal_project Project Module

tripal_pub/api/tripal_pub.DEPRECATED.inc

@@ -0,0 +1,423 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal analysis api
+ */
+
+/**
+ * @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 pub_search_remote().
+ *
+ * @see pub_search_remote().
+ */
+function tripal_pub_get_remote_search_results($remote_db, $search_array, $num_to_retrieve, $page = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_get_remote_search_results',
+      '%new_function' => 'pub_search_remote'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_remote_pub_record().
+ *
+ * @see chado_get_remote_pub_record().
+ */
+function tripal_pub_get_raw_data($dbxref) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_get_raw_data',
+      '%new_function' => 'chado_get_remote_pub_record'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_update_multiple_publications().
+ *
+ * @see chado_update_multiple_publications().
+ */
+function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db = NULL) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_update_publications',
+      '%new_function' => 'chado_update_multiple_publications'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_import_multiple_publications().
+ *
+ * @see chado_import_multiple_publications().
+ */
+function tripal_pub_import_publications_by_import_id($import_id, $job_id = NULL) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_import_publications_by_import_id',
+      '%new_function' => 'chado_import_multiple_publications'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_import_multiple_publications().
+ *
+ * @see chado_import_multiple_publications().
+ */
+function tripal_pub_import_publications($report_email = FALSE, $do_update = FALSE) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_import_publications',
+      '%new_function' => 'chado_import_multiple_publications'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_import_multiple_publications().
+ *
+ * @see chado_import_multiple_publications().
+ */
+function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_import_by_dbxref',
+      '%new_function' => 'chado_import_multiple_publications'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_multiple_publications().
+ *
+ * @see chado_insert_multiple_publications().
+ */
+function tripal_pub_add_publications($pubs, $do_contact, $update = FALSE) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_add_publications',
+      '%new_function' => 'chado_insert_multiple_publications'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_associate_dbxref().
+ *
+ * @see chado_associate_dbxref().
+ */
+function tripal_pub_add_pub_dbxref($pub_id, $pub_dbxref) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_add_pub_dbxref',
+      '%new_function' => 'chado_associate_dbxref'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_publication().
+ *
+ * @see chado_get_publication().
+ */
+function tripal_pub_get_pubs_by_dbxref($pub_dbxref) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_get_pubs_by_dbxref',
+      '%new_function' => 'chado_get_publication'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_get_publication().
+ *
+ * @see chado_get_publication().
+ */
+function tripal_pub_get_pubs_by_title_type_pyear_series($title, $type = NULL, $pyear = NULL, $series_name = NULL) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_get_pubs_by_title_type_pyear_series',
+      '%new_function' => 'chado_get_publication'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_publication().
+ *
+ * @see chado_get_publication().
+ */
+function tripal_pub_get_pub_by_uniquename($name) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_get_pub_by_uniquename',
+      '%new_function' => 'chado_get_publication'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_insert_publication().
+ *
+ * @see chado_insert_publication().
+ */
+function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE, $update_if_exists = FALSE) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_add_publication',
+      '%new_function' => 'chado_insert_publication'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_multiple_pubauthors().
+ *
+ * @see chado_insert_multiple_pubauthors().
+ */
+function tripal_pub_add_authors($pub_id, $authors, $do_contact) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_add_authors',
+      '%new_function' => 'chado_insert_multiple_pubauthors'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_property().
+ *
+ * @see chado_get_property().
+ */
+function tripal_pub_get_property($pub_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_get_property',
+      '%new_function' => 'chado_get_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_insert_property().
+ *
+ * @see chado_insert_property().
+ */
+function tripal_pub_insert_property($pub_id, $property, $value, $update_if_present = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_insert_property',
+      '%new_function' => 'chado_insert_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
+ */
+function tripal_pub_update_property($pub_id, $property, $value, $insert_if_missing = 0) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_update_property',
+      '%new_function' => 'chado_update_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
+ */
+function tripal_pub_delete_property($pub_id, $property) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_delete_property',
+      '%new_function' => 'chado_delete_property'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_publication().
+ *
+ * @see chado_get_publication().
+ */
+function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_get_publication_array',
+      '%new_function' => 'chado_get_publication'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by pub_generate_citation().
+ *
+ * @see pub_generate_citation().
+ */
+function tripal_pub_create_citation($pub) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_pub_create_citation',
+      '%new_function' => 'pub_generate_citation'
+    )
+  );
+
+  return FALSE;
+}

tripal_pub/tripal_pub.module

@@ -5,6 +5,7 @@
  */
 
 require_once 'api/tripal_pub.api.inc';
+//require_once 'api/tripal_pub.DEPRECATED.inc';
 
 require_once 'theme/tripal_pub.theme.inc';
 

tripal_stock/api/tripal_stock.DEPRECATED.inc

@@ -0,0 +1,137 @@
+<?php
+/**
+ * @file
+ * Wrapper functions to provide backwards compatibility for the tripal stock api
+ */
+
+/**
+ * @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_get_stock().
+ *
+ * @see chado_get_stock().
+ */
+function tripal_stock_get_stock_by_nid($nid) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_stock_get_stock_by_nid',
+      '%new_function' => 'chado_get_stock'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_stock().
+ *
+ * @see chado_get_stock().
+ */
+function tripal_stock_get_stock_by_stock_id($stock_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_stock_get_stock_by_stock_id',
+      '%new_function' => 'chado_get_stock'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_get_multiple_stocks().
+ *
+ * @see chado_get_multiple_stocks().
+ */
+function tripal_stock_get_all_stocks() {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_stock_get_all_stocks',
+      '%new_function' => 'chado_get_multiple_stocks'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @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_get_multiple_stocks().
+ *
+ * @see chado_get_multiple_stocks().
+ */
+function tripal_stock_get_stocks($values) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_stock_get_stocks',
+      '%new_function' => 'chado_get_multiple_stocks'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_stock().
+ *
+ * @see chado_get_stock().
+ */
+function tripal_stock_get_stocks_by_stockprop($stockprop_values, $stock_values) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_stock_get_stocks_by_stockprop',
+      '%new_function' => 'chado_get_stock'
+    )
+  );
+
+  return FALSE;
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_stock().
+ *
+ * @see chado_get_stock().
+ */
+function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
+
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_stock_get_stock_by_name_identifier',
+      '%new_function' => 'chado_get_stock'
+    )
+  );
+
+  return FALSE;
+}

tripal_stock/tripal_stock.module

@@ -5,6 +5,7 @@
  */
 
 require_once 'api/tripal_stock.api.inc';
+//require_once 'api/tripal_stock.DEPRECATED.inc';
 
 require_once 'theme/tripal_stock.theme.inc';