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@@ -48,6 +48,337 @@ class GFF3ImporterTest extends TripalTestCase {
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$this->assertEquals($name, $query);
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}
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+ /**
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+ * Run the GFF loader on small_gene.gff for testing.
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+ *
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+ * This gff has many attributes that we would like to test in the
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+ * testGFFImporterAttribute*() methods.
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+ */
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+ private function initGFFImporterAttributes() {
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+ $gff = ['file_local' => __DIR__ . '/../data/small_gene.gff'];
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+ $fasta = ['file_local' => __DIR__ . '/../data/short_scaffold.fasta'];
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+ $analysis = factory('chado.analysis')->create();
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+ $organism = factory('chado.organism')->create();
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+ $run_args = [
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+ 'analysis_id' => $analysis->analysis_id,
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+ 'organism_id' => $organism->organism_id,
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+ 'use_transaction' => 1,
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+ 'add_only' => 0,
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+ 'update' => 1,
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+ 'create_organism' => 0,
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+ 'create_target' => 0,
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+ ///regexps for mRNA and protein.
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+ 're_mrna' => NULL,
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+ 're_protein' => NULL,
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+ //optional
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+ 'target_organism_id' => $organism->organism_id,
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+ 'target_type' => NULL,
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+ 'start_line' => NULL,
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+ 'landmark_type' => NULL,
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+ 'alt_id_attr' => NULL,
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+ ];
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+ $this->loadLandmarks($analysis, $organism, $fasta);
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+ $this->runGFFLoader($run_args, $gff);
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+ $this->organism = $organism;
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+ $this->analysis = $analysis;
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+ $this->gene_cvt = chado_get_cvterm(array(
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+ 'name' => 'gene',
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+ 'cv_id' => array(
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+ 'name' => 'sequence',
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+ ),
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+ ))->cvterm_id;
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+ $this->mrna_cvt = chado_get_cvterm(array(
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+ 'name' => 'mRNA',
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+ 'cv_id' => array(
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+ 'name' => 'sequence',
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+ ),
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+ ))->cvterm_id;
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+ $this->gene_1_uname = 'test_gene_001';
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+ $this->gene_2_uname = 'test_gene_002';
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+ }
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+
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+ /**
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+ * Ensures that the feature record is loaded correctly into chado.
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+ *
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+ * @group gff
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+ */
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+ public function testGFFImporterAttributeFeature() {
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+ $this->initGFFImporterAttributes();
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+ $organism = $this->organism;
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+
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+ $query = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $this->gene_1_uname)
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+ ->condition('type_id', $this->gene_cvt)
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+ ->execute();
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+
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+ $gene_1 = $query->fetchObject();
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+ $this->assertEquals('test_gene_001', $gene_1->uniquename);
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+ $this->assertEquals('test_gene_001', $gene_1->name);
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+ $this->assertEquals($organism->organism_id, $gene_1->organism_id);
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+ $this->assertEquals($this->gene_cvt, $gene_1->type_id);
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+ }
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+
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+ /**
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+ * Ensures the feature alias is loaded correctly into chado.
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+ *
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+ * @group gff
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+ */
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+ public function testGFFImporterAttributeAlias() {
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+ $this->initGFFImporterAttributes();
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+ $alias = 'first_test_gene';
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+
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+ $gene_1 = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $this->gene_1_uname)
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+ ->condition('type_id', $this->gene_cvt)
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+ ->execute()->fetchObject();
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+
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+ $query = db_select('chado.feature_synonym', 'fs');
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+ $query->join('chado.synonym', 's', 's.synonym_id = fs.synonym_id');
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+ $query->fields('s');
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+ $query->condition('fs.feature_id', $gene_1->feature_id);
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+ $query = $query->execute();
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+ $result = $query->fetchObject();
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+ $this->assertEquals($alias, $result->name);
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+ }
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+
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+ /**
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+ * Ensures that the dbxref records are loaded correctly into chado.
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+ *
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+ * @group gff
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+ */
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+ public function testGFFImporterAttributeDbxref() {
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+ $this->initGFFImporterAttributes();
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+ $test_db_name = 'TEST_DB';
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+ $dbx_accession = 'test_gene_dbx_001';
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+ $test_db = chado_get_db(array('name' => $test_db_name));
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+ $gff_db = chado_get_db(array('name' => 'GFF_source'));
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+
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+ $gene_1 = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $this->gene_1_uname)
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+ ->condition('type_id', $this->gene_cvt)
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+ ->execute()->fetchObject();
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+
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+ $dbx_query = db_select('chado.feature_dbxref', 'fdbx');
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+ $dbx_query->join('chado.dbxref', 'dbx', 'dbx.dbxref_id = fdbx.dbxref_id');
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+ $dbx_query->fields('dbx');
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+ $dbx_query->condition('fdbx.feature_id', $gene_1->feature_id);
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+ $gff_query = clone $dbx_query;
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+
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+ $dbx_query->condition('dbx.db_id', $test_db->db_id);
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+ $dbx_query = $dbx_query->execute();
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+
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+ $gff_query->condition('dbx.db_id', $gff_db->db_id);
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+ $gff_query = $gff_query->execute();
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+
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+ $dbxref = $dbx_query->fetchObject();
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+ $gff_dbxref = $gff_query->fetchObject();
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+ $this->assertEquals($dbx_accession, $dbxref->accession);
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+ $this->assertEquals($this->gene_1_uname, $gff_dbxref->accession);
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+ }
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+
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+ /**
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+ * Ensures ontology term records loaded correctly into chado.
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+ *
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+ * @group gff
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+ */
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+ public function testGFFImporterAttributeOntology() {
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+ $this->initGFFImporterAttributes();
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+ $ontology_db = 'SO';
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+ $ontology_accession = '0000704';
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+
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+ $gene_1 = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $this->gene_1_uname)
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+ ->condition('type_id', $this->gene_cvt)
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+ ->execute()->fetchObject();
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+
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+ $term = chado_get_cvterm(array(
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+ 'dbxref_id' => array(
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+ 'accession' => $ontology_accession,
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+ 'db_id' => array(
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+ 'name' => $ontology_db,
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+ ),
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+ ),
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+ ));
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+
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+ $feature_cvt = db_select('chado.feature_cvterm', 'fcvt')
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+ ->fields('fcvt')
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+ ->condition('cvterm_id', $term->cvterm_id)
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+ ->condition('feature_id', $gene_1->feature_id)
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+ ->execute();
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+ $this->assertEquals(1, $feature_cvt->rowCount());
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+ }
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+
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+ /**
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+ * Ensures feature parent record loaded correctly into chado.
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+ *
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+ * @group gff
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+ */
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+ public function testGFFImporterAttributeParent() {
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+ $this->initGFFImporterAttributes();
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+ $mrna_uname = 'test_mrna_001.1';
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+
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+ $rel_cvt = chado_get_cvterm(array(
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+ 'name' => 'part_of',
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+ 'cv_id' => array(
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+ 'name' => 'sequence',
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+ ),
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+ ))->cvterm_id;
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+
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+ $mrna = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $mrna_uname)
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+ ->condition('type_id', $this->mrna_cvt)
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+ ->execute()->fetchObject();
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+
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+ $query = db_select('chado.feature_relationship', 'fr');
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+ $query->join('chado.feature', 'f', 'f.feature_id = fr.object_id');
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+ $query->fields('f');
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+ $query->condition('fr.subject_id', $mrna->feature_id);
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+ $query->condition('fr.type_id', $rel_cvt);
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+ $query = $query->execute();
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+ $parent = $query->fetchObject();
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+
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+ $this->assertEquals('test_gene_001', $parent->uniquename);
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+ $this->assertEquals('test_gene_001', $parent->name);
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+ $this->assertEquals($this->gene_cvt, $parent->type_id);
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+ $this->assertEquals($this->organism->organism_id, $parent->organism_id);
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+ }
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+
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+ /**
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+ * Ensure target record loaded correctly into chado.
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+ *
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+ * @group gff
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+ */
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+ public function testGFFImporterAttributeTarget() {
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+ $this->initGFFImporterAttributes();
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+ $target_feature = 'scaffold1';
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+ $start = 99;
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+ $end = 200;
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+ $target_type = 'supercontig';
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+ $target_cvt = chado_get_cvterm(array(
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+ 'name' => $target_type,
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+ 'cv_id' => array(
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+ 'name' => 'sequence',
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+ ),
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+ ))->cvterm_id;
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+
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+ $source_feature = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $target_feature)
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+ ->condition('type_id', $target_cvt)
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+ ->execute()->fetchObject();
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+
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+ $gene_1 = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $this->gene_1_uname)
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+ ->condition('type_id', $this->gene_cvt)
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+ ->execute()->fetchObject();
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+
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+ $featureloc = db_select('chado.featureloc', 'fl')
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+ ->fields('fl')
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+ ->condition('fl.feature_id', $gene_1->feature_id)
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+ ->condition('fl.srcfeature_id', $source_feature->feature_id)
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+ ->execute()->fetchObject();
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+
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+ $this->assertEquals($start, $featureloc->fmin);
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+ $this->assertEquals($end, $featureloc->fmax);
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+ }
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+
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+ /**
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+ * Ensure properties loaded correctly into chado.
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+ *
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+ * @group gff
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+ */
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+ public function testGFFImporterAttributeProperty() {
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+ $this->initGFFImporterAttributes();
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+ $gap_1 = 'test_gap_1';
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+ $gap_2 = 'test_gap_2';
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+ $note_val = 'test_gene_001_note';
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+
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+ $gene_1 = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $this->gene_1_uname)
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+ ->condition('type_id', $this->gene_cvt)
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+ ->execute()->fetchObject();
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+
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+ $gap_cvt = chado_get_cvterm(array(
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+ 'name' => 'Gap',
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+ 'cv_id' => array(
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+ 'name' => 'feature_property',
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+ ),
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+ ))->cvterm_id;
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+
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+ $note_cvt = chado_get_cvterm(array(
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+ 'name' => 'Note',
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+ 'cv_id' => array(
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+ 'name' => 'feature_property',
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+ ),
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+ ))->cvterm_id;
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+
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+ // Assert gaps loaded correctly
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+ $gaps_query = db_select('chado.featureprop', 'fp')
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+ ->fields('fp')
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+ ->condition('feature_id', $gene_1->feature_id)
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+ ->condition('type_id', $gap_cvt)
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+ ->execute();
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+
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+ while (($gap = $gaps_query->fetchObject())) {
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+ $gaps[$gap->value] = $gap;
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+ }
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+
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+ $this->assertEquals($gap_1, $gaps[$gap_1]->value);
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+ $this->assertEquals(0, $gaps[$gap_1]->rank);
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+ $this->assertEquals($gap_2, $gaps[$gap_2]->value);
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+ $this->assertEquals(1, $gaps[$gap_2]->rank);
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+
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+ // Assert note loaded correctly
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+ $note = db_select('chado.featureprop', 'fp')
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+ ->fields('fp')
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+ ->condition('feature_id', $gene_1->feature_id)
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+ ->condition('type_id', $note_cvt)
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+ ->execute()->fetchObject();
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+
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+ $this->assertEquals($note_val, $note->value);
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+ $this->assertEquals(0, $note->rank);
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+ }
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+
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+ /**
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+ * Ensure derives from information loaded correctly into chado.
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+ *
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+ * @group gff
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+ */
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+ public function testGFFImporterAttributeDerivesFrom() {
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+ $this->initGFFImporterAttributes();
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+
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+ $gene_2 = db_select('chado.feature', 'f')
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+ ->fields('f')
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+ ->condition('uniquename', $this->gene_2_uname)
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+ ->condition('type_id', $this->gene_cvt)
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+ ->execute()->fetchObject();
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+
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+ $derivesfrom_cvt = chado_get_cvterm(array(
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+ 'name' => 'derives_from',
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+ 'cv_id' => array(
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+ 'name' => 'sequence',
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+ ),
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+ ))->cvterm_id;
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+
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+ $query = db_select('chado.feature', 'f');
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+ $query->join('chado.feature_relationship', 'fr', 'f.feature_id = fr.object_id');
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+ $query->fields('f');
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+ $query->condition('fr.subject_id', $gene_2->feature_id);
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+ $query->condition('fr.type_id', $derivesfrom_cvt);
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+ $query = $query->execute();
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+ $derivesfrom_feature = $query->fetchObject();
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+
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+ $this->assertEquals($this->gene_1_uname, $derivesfrom_feature->uniquename);
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+ $this->assertEquals($this->gene_1_uname, $derivesfrom_feature->name);
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+ $this->assertEquals($this->gene_cvt, $derivesfrom_feature->type_id);
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+ }
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/**
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* Add a skip protein option. Test that when checked, implicit proteins are
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@@ -175,8 +506,10 @@ class GFF3ImporterTest extends TripalTestCase {
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// });
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}
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- private function loadLandmarks($analysis, $organism) {
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- $landmark_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/sequences/empty_landmarks.fasta'];
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+ private function loadLandmarks($analysis, $organism, $landmark_file = array()) {
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+ if (empty($landmark_file)) {
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+ $landmark_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/sequences/empty_landmarks.fasta'];
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+ }
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$run_args = [
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'organism_id' => $organism->organism_id,
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Peter Richter