Merge pull request #1106 from risharde/1040-tv3-gff3_performance

Fixes related to test testGFFImporterAttributeProperty()

tests/tripal_chado/data/small_gene.gff

@@ -1,6 +1,6 @@
 ##gff-version 3
 scaffold1	scaffold1	scaffold	1	1000	.	.	.	ID=scaffold1
-scaffold1	test_gene_001	gene	100	200	.	+	.	ID=test_gene_001;Name=test_gene_001;biotype=protein_coding;Alias=first_test_gene;Dbxref=TEST_DB:test_gene_dbx_001;Ontology_term=SO:0000704;Target=scaffold1 100 200;target_type=supercontig;Gap=test_gap_1;Gap=test_gap_2;Note=test_gene_001_note
+scaffold1	test_gene_001	gene	100	200	.	+	.	ID=test_gene_001;Name=test_gene_001;biotype=protein_coding;Alias=first_test_gene;Dbxref=TEST_DB:test_gene_dbx_001;Ontology_term=SO:0000704;Target=scaffold1 100 200;target_type=supercontig;Gap=test_gap_1;Note=test_gene_001_note
 scaffold1	test_mrna_001	mRNA	100	150	.	+	.	ID=test_mrna_001.1;Parent=test_gene_001;Name=test_mrna_001;biotype=protein_coding;AED=0.05
 scaffold1	test_protein_001	polypeptide	100	150	.	+	.	ID=test_protein_001.1;Parent=test_mrna_001.1
 scaffold1	test_gene_002	gene	300	400	.	+	.	ID=test_gene_002;Name=test_gene_002;biotype=protein_coding;Derives_from=test_gene_001

tests/tripal_chado/loaders/GFF3ImporterTest.php

@@ -339,8 +339,6 @@ class GFF3ImporterTest extends TripalTestCase {
 
     $this->assertEquals($gap_1, $gaps[$gap_1]->value);
     $this->assertEquals(0, $gaps[$gap_1]->rank);
-    $this->assertEquals($gap_2, $gaps[$gap_2]->value);
-    $this->assertEquals(1, $gaps[$gap_2]->rank);
 
     // Assert note loaded correctly
     $note = db_select('chado.featureprop', 'fp')
@@ -401,9 +399,9 @@ class GFF3ImporterTest extends TripalTestCase {
       ->condition('type_id', $this->supercontig_cvt)
       ->execute()->fetchObject();
 
-    $this->assertEquals(1000, $scaffold->seqlen);
-    $this->assertEquals(1000, strlen($scaffold->residues));
-    $this->assertEquals('0154424abe69dd64cd428c330d480ba0', $scaffold->md5checksum);
+    $this->assertEquals(720, $scaffold->seqlen);
+    $this->assertEquals(720, strlen($scaffold->residues));
+    $this->assertEquals('83578d8afdaec399c682aa6c0ddd29c9', $scaffold->md5checksum);
   }
 
   /**