Added a function that lists all tables in a Chado schema (per version) and altered the core to use that function. Previously it used a Postgres SQL statement to pull out all tables in the schema but this caused problems when non Chado tables were also present in the schema.

tripal_core/api/tripal_core.api.inc

@@ -2816,24 +2816,24 @@ function tripal_core_chado_schema_exists() {
  */
 function tripal_core_get_chado_tables($include_custom = NULL) {
 
-  if (is_array($db_url) AND array_key_exists('chado', $db_url)) {
-    $previous_db = tripal_db_set_active('chado');
-    // @coder-ignore: acting on pg_catalog schema rather then drupal schema therefore, table prefixing does not apply
-    $sql = 'SELECT tablename FROM pg_tables';
-    $resource = db_query($sql);
-    tripal_db_set_active($previous_db);
-  }
-  else {
-    // @coder-ignore: acting on pg_catalog schema rather then drupal schema therefore, table prefixing does not apply
-    $sql = "SELECT tablename FROM pg_tables WHERE schemaname='chado'";
-    $resource = db_query($sql);
-  }
-
+	
+	// first get the chado version that is installed
+  $v = tripal_core_get_chado_version();
+  
   $tables = array();
-  while ($r = db_fetch_object($resource)) {
-    $tables[$r->tablename] = $r->tablename;
+  if ($v == '1.2') {
+    $tables_v1_2 = tripal_core_chado_get_v1_2_tables();
+    foreach ($tables_v1_2 as $table) {
+      $tables[$table] = $table;
+    }
   }
-
+  if ($v == '1.11' or $v == '1.11 or older') {
+    $tables_v1_11 = tripal_core_chado_get_v1_11_tables();
+    foreach ($tables_v1_11 as $table) {
+      $tables[$table] = $table;
+    }
+  }
+  
   // now add in the custom tables too
   if ($include_custom) {
     $sql = "SELECT table_name FROM {tripal_custom_tables}";

tripal_core/api/tripal_core.schema_v1.11.api.inc

@@ -10751,3 +10751,161 @@ function tripal_core_chado_schema_v1_11_treatment() {
   );
   return $description;
 }
+
+/**
+ * Lists the table names in the v1.11 chado schema
+ *
+ * @return
+ *    An array containing all of the table names
+ *
+ * @ingroup tripal_chado_v1.2_schema_api
+ *
+ */
+function tripal_core_chado_get_v1_11_tables() {
+  $tables = array(
+		'acquisition',
+		'acquisition_relationship',
+		'acquisitionprop',
+		'analysis',
+		'analysisfeature',
+		'analysisfeatureprop',
+		'analysisprop',
+		'arraydesign',
+		'arraydesignprop',
+		'assay',
+		'assay_biomaterial',
+		'assay_project',
+		'assayprop',
+		'biomaterial',
+		'biomaterial_dbxref',
+		'biomaterial_relationship',
+		'biomaterial_treatment',
+		'biomaterialprop',
+		'cell_line',
+		'cell_line_cvterm',
+		'cell_line_cvtermprop',
+		'cell_line_dbxref',
+		'cell_line_feature',
+		'cell_line_library',
+		'cell_line_pub',
+		'cell_line_relationship',
+		'cell_line_synonym',
+		'cell_lineprop',
+		'cell_lineprop_pub',
+		'channel',
+		'contact',
+		'contact_relationship',
+		'control',
+		'cv',
+		'cvterm',
+		'cvterm_dbxref',
+		'cvterm_relationship',
+		'cvtermpath',
+		'cvtermprop',
+		'cvtermsynonym',
+		'db',
+		'dbxref',
+		'dbxrefprop',
+		'eimage',
+		'element',
+		'element_relationship',
+		'elementresult',
+		'elementresult_relationship',
+		'environment',
+		'environment_cvterm',
+		'expression',
+		'expression_cvterm',
+		'expression_cvtermprop',
+		'expression_image',
+		'expression_pub',
+		'expressionprop',
+		'feature',
+		'feature_cvterm',
+		'feature_cvterm_dbxref',
+		'feature_cvterm_pub',
+		'feature_cvtermprop',
+		'feature_dbxref',
+		'feature_expression',
+		'feature_expressionprop',
+		'feature_genotype',
+		'feature_phenotype',
+		'feature_pub',
+		'feature_pubprop',
+		'feature_relationship',
+		'feature_relationship_pub',
+		'feature_relationshipprop',
+		'feature_relationshipprop_pub',
+		'feature_synonym',
+		'featureloc',
+		'featureloc_pub',
+		'featuremap',
+		'featuremap_pub',
+		'featurepos',
+		'featureprop',
+		'featureprop_pub',
+		'featurerange',
+		'genotype',
+		'library',
+		'library_cvterm',
+		'library_dbxref',
+		'library_feature',
+		'library_pub',
+		'library_synonym',
+		'libraryprop',
+		'libraryprop_pub',
+		'magedocumentation',
+		'mageml',
+		'materialized_view',
+		'organism',
+		'organism_dbxref',
+		'organismprop',
+		'phendesc',
+		'phenotype',
+		'phenotype_comparison',
+		'phenotype_comparison_cvterm',
+		'phenotype_cvterm',
+		'phenstatement',
+		'phylonode',
+		'phylonode_dbxref',
+		'phylonode_organism',
+		'phylonode_pub',
+		'phylonode_relationship',
+		'phylonodeprop',
+		'phylotree',
+		'phylotree_pub',
+		'project',
+		'protocol',
+		'protocolparam',
+		'pub',
+		'pub_dbxref',
+		'pub_relationship',
+		'pubauthor',
+		'pubprop',
+		'quantification',
+		'quantification_relationship',
+		'quantificationprop',
+		'stock',
+		'stock_cvterm',
+		'stock_dbxref',
+		'stock_genotype',
+		'stock_pub',
+		'stock_relationship',
+		'stock_relationship_pub',
+		'stockcollection',
+		'stockcollection_stock',
+		'stockcollectionprop',
+		'stockprop',
+		'stockprop_pub',
+		'study',
+		'study_assay',
+		'studydesign',
+		'studydesignprop',
+		'studyfactor',
+		'studyfactorvalue',
+		'studyprop',
+		'studyprop_feature',
+		'synonym',
+		'tableinfo',
+		'treatment'
+  );
+}

tripal_core/api/tripal_core.schema_v1.2.api.inc

@@ -13993,3 +13993,191 @@ function tripal_core_chado_schema_v1_2_treatment() {
   );
   return $description;
 }
+
+/**
+ * Lists the table names in the v1.2 chado schema
+ *
+ * @return
+ *    An array containing all of the table names
+ *
+ * @ingroup tripal_chado_v1.2_schema_api
+ *
+ */
+function tripal_core_chado_get_v1_2_tables() {
+  $tables = array(
+    'acquisition',
+		'acquisition_relationship',
+		'acquisitionprop',
+		'analysis',
+		'analysisfeature',
+		'analysisfeatureprop',
+		'analysisprop',
+		'arraydesign',
+		'arraydesignprop',
+		'assay',
+		'assay_biomaterial',
+		'assay_project',
+		'assayprop',
+		'biomaterial',
+		'biomaterial_dbxref',
+		'biomaterial_relationship',
+		'biomaterial_treatment',
+		'biomaterialprop',
+		'cell_line',
+		'cell_line_cvterm',
+		'cell_line_cvtermprop',
+		'cell_line_dbxref',
+		'cell_line_feature',
+		'cell_line_library',
+		'cell_line_pub',
+		'cell_line_relationship',
+		'cell_line_synonym',
+		'cell_lineprop',
+		'cell_lineprop_pub',
+		'chadoprop',
+		'channel',
+		'contact',
+		'contact_relationship',
+		'control',
+		'cv',
+		'cvprop',
+		'cvterm',
+		'cvterm_dbxref',
+		'cvterm_relationship',
+		'cvtermpath',
+		'cvtermprop',
+		'cvtermsynonym',
+		'db',
+		'dbxref',
+		'dbxrefprop',
+		'eimage',
+		'element',
+		'element_relationship',
+		'elementresult',
+		'elementresult_relationship',
+		'environment',
+		'environment_cvterm',
+		'expression',
+		'expression_cvterm',
+		'expression_cvtermprop',
+		'expression_image',
+		'expression_pub',
+		'expressionprop',
+		'feature',
+		'feature_cvterm',
+		'feature_cvterm_dbxref',
+		'feature_cvterm_pub',
+		'feature_cvtermprop',
+		'feature_dbxref',
+		'feature_expression',
+		'feature_expressionprop',
+		'feature_genotype',
+		'feature_phenotype',
+		'feature_pub',
+		'feature_pubprop',
+		'feature_relationship',
+		'feature_relationship_pub',
+		'feature_relationshipprop',
+		'feature_relationshipprop_pub',
+		'feature_synonym',
+		'featureloc',
+		'featureloc_pub',
+		'featuremap',
+		'featuremap_pub',
+		'featurepos',
+		'featureprop',
+		'featureprop_pub',
+		'featurerange',
+		'genotype',
+		'genotypeprop',
+		'library',
+		'library_cvterm',
+		'library_dbxref',
+		'library_feature',
+		'library_pub',
+		'library_synonym',
+		'libraryprop',
+		'libraryprop_pub',
+		'magedocumentation',
+		'mageml',
+		'nd_experiment',
+		'nd_experiment_contact',
+		'nd_experiment_dbxref',
+		'nd_experiment_genotype',
+		'nd_experiment_phenotype',
+		'nd_experiment_project',
+		'nd_experiment_protocol',
+		'nd_experiment_pub',
+		'nd_experiment_stock',
+		'nd_experiment_stock_dbxref',
+		'nd_experiment_stockprop',
+		'nd_experimentprop',
+		'nd_geolocation',
+		'nd_geolocationprop',
+		'nd_protocol',
+		'nd_protocol_reagent',
+		'nd_protocolprop',
+		'nd_reagent',
+		'nd_reagent_relationship',
+		'nd_reagentprop',
+		'organism',
+		'organism_dbxref',
+		'organismprop',
+		'phendesc',
+		'phenotype',
+		'phenotype_comparison',
+		'phenotype_comparison_cvterm',
+		'phenotype_cvterm',
+		'phenstatement',
+		'phylonode',
+		'phylonode_dbxref',
+		'phylonode_organism',
+		'phylonode_pub',
+		'phylonode_relationship',
+		'phylonodeprop',
+		'phylotree',
+		'phylotree_pub',
+		'project',
+		'project_contact',
+		'project_pub',
+		'project_relationship',
+		'projectprop',
+		'protocol',
+		'protocolparam',
+		'pub',
+		'pub_dbxref',
+		'pub_relationship',
+		'pubauthor',
+		'pubprop',
+		'quantification',
+		'quantification_relationship',
+		'quantificationprop',
+		'stock',
+		'stock_cvterm',
+		'stock_cvtermprop',
+		'stock_dbxref',
+		'stock_dbxrefprop',
+		'stock_genotype',
+		'stock_pub',
+		'stock_relationship',
+		'stock_relationship_cvterm',
+		'stock_relationship_pub',
+		'stockcollection',
+		'stockcollection_stock',
+		'stockcollectionprop',
+		'stockprop',
+		'stockprop_pub',
+		'study',
+		'study_assay',
+		'studydesign',
+		'studydesignprop',
+		'studyfactor',
+		'studyfactorvalue',
+		'studyprop',
+		'studyprop_feature',
+		'synonym',
+		'tableinfo',
+		'treatment'
+   );	
+   return $tables;
+}

tripal_views/api/tripal_views.api.inc

@@ -187,7 +187,7 @@ function tripal_views_integration_add_entry($defn_array) {
   }
   else {
     $status = FALSE;
-    drupal_set_message(t('Unable to integrate %table table due to a missing name or comment field.', array('%table' => $defn_array['table'])), 'error');
+    drupal_set_message(t('Unable to integrate "%table" table due to a missing name or comment field.', array('%table' => $defn_array['table'])), 'error');
   }
 
   if ($status) {

tripal_views/tripal_views.views.inc

@@ -231,7 +231,6 @@ function tripal_views_views_data() {
     ),
   );
 
-
   $tvi_query = db_query('SELECT * FROM {tripal_views}');
 
   while ($tvi_row = db_fetch_object($tvi_query)) {
@@ -285,6 +284,7 @@ function tripal_views_views_data() {
         $base_fields[$field->column_name]['help'] = $field->description;
       }
     }
+    // if this is not a legacy materialized view
     else {
       $base_table = $tvi_row->table_name;