Fixed schema to make it compliant.

tests/tripal_chado/api/ChadoComplianceTest.php

@@ -88,12 +88,15 @@ class ChadoComplianceTest extends TripalTestCase {
 
     // For the primary key:
     // Check #4: The constraint exists.
-    $pkey_column = $table_schema['primary key'][0];
-    $this->assertTrue(
-      $chado_schema->checkPrimaryKey($table_name, $pkey_column),
-      t('The column "!table.!column" must have an associated sequence attached for chado v!version.',
-        array('!column' => $pkey_column, '!table' => $table_name, '!version' => $version))
-    );
+    if (isset($table_schema['primary key']) AND !empty($table_schema['primary key'])) {
+      $pkey_column = $table_schema['primary key'][0];
+      $pkey_compliance = $chado_schema->checkPrimaryKey($table_name, $pkey_column);
+      $this->assertTrue(
+        $pkey_compliance,
+        t('The column "!table.!column" must have an associated sequence attached for chado v!version.',
+          array('!column' => $pkey_column, '!table' => $table_name, '!version' => $version))
+      );
+    }
 
     // For each unique key:
     foreach ($table_schema['unique keys'] as $constraint_name => $columns) {

tests/tripal_chado/api/ChadoSchemaTest.php

@@ -140,19 +140,25 @@ class ChadoSchemaTest extends TripalTestCase {
         array('!table' => $table_name))
     );
 
+    // Instead of asserting these keys exist. Lets assert that if they do exist,
+    // they match the expected format.
+
+/*
     $this->assertArrayHasKey(
       'primary key',
       $table_schema,
       t('The schema array for "!table" should have the primary key listed in an "primary key" array',
         array('!table' => $table_name))
     );
-
+*/
+/*
     $this->assertArrayHasKey(
       'unique keys',
       $table_schema,
       t('The schema array for "!table" should have unique keys listed in an "unique keys" array',
         array('!table' => $table_name))
     );
+*/
 
     $this->assertArrayHasKey(
       'foreign keys',

tripal_chado/api/ChadoSchema.inc

@@ -526,6 +526,18 @@ class ChadoSchema {
       $column = $table_schema['primary key'][0];
     }
 
+    // If there is no primary key then we can't check it.
+    // It neither passes nore fails validation.
+    if (empty($column)) {
+      tripal_report_error(
+        'ChadoSchema',
+        TRIPAL_NOTICE,
+        'Cannot check the validity of the primary key for "!table" since there is no record of one.',
+        array('!table' => $table)
+      );
+      return NULL;
+    }
+
     // Check the column exists.
     $column_exists = $this->checkColumnExists($table, $column);
     if (!$column_exists) {

tripal_chado/api/tripal_chado.schema_v1.3.api.inc

@@ -4118,7 +4118,7 @@ function tripal_chado_chado_schema_v1_3_cvtermprop() {
       ),
     ),
     'unique keys' => array(
-      'cvterm_id_type_id_value_rank' => array(
+      'cvtermprop_cvterm_id_type_id_value_rank_key' => array(
         0 => 'cvterm_id',
         1 => 'type_id',
         2 => 'value',
@@ -7019,13 +7019,14 @@ function tripal_chado_chado_schema_v1_3_featuremap_dbxref() {
         'default' => 'true',
       ),
     ),
-    // TODO: this unique constraint is missing from the actual Chado schema.
-    // It should be included.
     'unique keys' => array(
+      /* @todo: this unique constraint is missing from the actual Chado schema.
+          It should be included.
       'feature_dbxref_c1' => array(
         0 => 'featuremap_id',
         1 => 'dbxref_id',
       ),
+      */
     ),
     'indexes' => array(
       'featuremap_dbxref_idx1' => array(
@@ -7252,13 +7253,14 @@ function tripal_chado_chado_schema_v1_3_featuremap_pub() {
         'not null' => TRUE,
       ),
     ),
-    // TODO: this unique constraint is missing from the actual Chado schema.
-    // It should be included.
     'unique keys' => array(
+      /* @todo: this unique constraint is missing from the actual Chado schema.
+          It should be included.
       'feature_pub_c1' => array(
         0 => 'featuremap_id',
         1 => 'pub_id',
       ),
+      */
     ),
     'indexes' => array(
       'featuremap_pub_idx1' => array(
@@ -9936,7 +9938,7 @@ function tripal_chado_chado_schema_v1_3_materialized_view() {
       ),
     ),
     'unique keys' => array(
-      'name' => array(
+      'materialized_view_name_key' => array(
         0 => 'name',
       ),
     ),
@@ -11123,7 +11125,7 @@ function tripal_chado_chado_schema_v1_3_nd_protocol() {
       ),
     ),
     'unique keys' => array(
-      'name' => array(
+      'nd_protocol_name_key' => array(
         0 => 'name',
       ),
     ),
@@ -13094,11 +13096,11 @@ function tripal_chado_chado_schema_v1_3_phylonode() {
       ),
     ),
     'unique keys' => array(
-      'phylotree_id_left_idx' => array(
+      'phylonode_phylotree_id_left_idx_key' => array(
         0 => 'phylotree_id',
         1 => 'left_idx',
       ),
-      'phylotree_id_right_idx' => array(
+      'phylonode_phylotree_id_right_idx_key' => array(
         0 => 'phylotree_id',
         1 => 'right_idx',
       ),
@@ -13189,7 +13191,7 @@ function tripal_chado_chado_schema_v1_3_phylonode_dbxref() {
       ),
     ),
     'unique keys' => array(
-      'phylonode_id_dbxref_id' => array(
+      'phylonode_dbxref_phylonode_id_dbxref_id_key' => array(
         0 => 'phylonode_id',
         1 => 'dbxref_id',
       ),
@@ -13262,7 +13264,7 @@ function tripal_chado_chado_schema_v1_3_phylonode_organism() {
       ),
     ),
     'unique keys' => array(
-      'phylonode_id' => array(
+      'phylonode_organism_phylonode_id_key' => array(
         0 => 'phylonode_id',
       ),
     ),
@@ -13346,7 +13348,7 @@ function tripal_chado_chado_schema_v1_3_phylonodeprop() {
       ),
     ),
     'unique keys' => array(
-      'phylonode_id_type_id_value_rank' => array(
+      'phylonodeprop_phylonode_id_type_id_value_rank_key' => array(
         0 => 'phylonode_id',
         1 => 'type_id',
         2 => 'value',
@@ -13421,7 +13423,7 @@ function tripal_chado_chado_schema_v1_3_phylonode_pub() {
       ),
     ),
     'unique keys' => array(
-      'phylonode_id_pub_id' => array(
+      'phylonode_pub_phylonode_id_pub_id_key' => array(
         0 => 'phylonode_id',
         1 => 'pub_id',
       ),
@@ -13515,7 +13517,7 @@ function tripal_chado_chado_schema_v1_3_phylonode_relationship() {
       0 => 'phylonode_relationship_id',
     ),
     'unique keys' => array(
-      'subject_id_object_id_type_id' => array(
+      'phylonode_relationship_subject_id_object_id_type_id_key' => array(
         0 => 'subject_id',
         1 => 'object_id',
         2 => 'type_id',
@@ -13768,7 +13770,7 @@ function tripal_chado_chado_schema_v1_3_phylotree_pub() {
       ),
     ),
     'unique keys' => array(
-      'phylotree_id_pub_id' => array(
+      'phylotree_pub_phylotree_id_pub_id_key' => array(
         0 => 'phylotree_id',
         1 => 'pub_id',
       ),
@@ -17676,7 +17678,7 @@ function tripal_chado_chado_schema_v1_3_studyprop() {
       0 => 'studyprop_id',
     ),
     'unique keys' => array(
-      'study_id_type_id_rank' => array(
+      'studyprop_study_id_type_id_rank_key' => array(
         0 => 'study_id',
         1 => 'type_id',
         2 => 'rank',
@@ -17756,7 +17758,7 @@ function tripal_chado_chado_schema_v1_3_studyprop_feature() {
       0 => 'studyprop_feature_id',
     ),
     'unique keys' => array(
-      'studyprop_id_feature_id' => array(
+      'studyprop_feature_studyprop_id_feature_id_key' => array(
         0 => 'studyprop_id',
         1 => 'feature_id',
       ),