<?php
namespace Tests;
use StatonLab\TripalTestSuite\DBTransaction;
use StatonLab\TripalTestSuite\TripalTestCase;
class OBOImporterTest extends TripalTestCase {
// Uncomment to auto start and rollback db transactions per test method.
use DBTransaction;
/**
* A helper function for loading any OBO.
*
* @param $name - ontology name. This goes in the tripal_cv_obo table.
* @param $path - path to the OBO. this can be a file path or a URL.
*
* @throws \Exception
*/
private function loadOBO($name, $path) {
$obo_id = db_select('public.tripal_cv_obo', 't')
->fields('t', ['obo_id'])
->condition('t.name', $name)
->execute()
->fetchField();
if (!$obo_id) {
$obo_id = db_insert('public.tripal_cv_obo')
->fields(['name' => $name, 'path' => $path])
->execute();
}
$run_args = ['obo_id' => $obo_id];
module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/OBOImporter');
$importer = new \OBOImporter();
$importer->create($run_args);
$importer->prepareFiles();
$importer->run();
}
/**
* Tests that an OBO from a remote URL can be loaded.
*
* For this test we will use the GO Plant Slim.
*
* @group obo
*/
public function testRemoteOBO() {
$name = 'core_test_goslim_plant';
$path = 'http://www.geneontology.org/ontology/subsets/goslim_plant.obo';
$this->loadOBO($name, $path);
// Test that we get all three vocabularies added: biological_process,
// cellular_component and molecular_function.
$bp_cv_id = db_select('chado.cv', 'c')
->fields('c', ['cv_id'])
->condition('name', 'biological_process')
->execute()
->fetchField();
$this->assertNotFalse($bp_cv_id,
"Missing the 'biological_process' cv record after loading the GO plant slim.");
$cc_cv_id = db_select('chado.cv', 'c')
->fields('c', ['cv_id'])
->condition('name', 'cellular_component')
->execute()
->fetchField();
$this->assertNotFalse($cc_cv_id,
"Missing the 'cellular_component' cv record after loading the GO plant slim.");
$mf_cv_id = db_select('chado.cv', 'c')
->fields('c', ['cv_id'])
->condition('name', 'molecular_function')
->execute()
->fetchField();
$this->assertNotFalse($mf_cv_id,
"Missing the 'molecular_function' cv record after loading the GO plant slim.");
// Make sure we have a proper database record.
$go_db_id = db_select('chado.db', 'd')
->fields('d', ['db_id'])
->condition('name', 'GO')
->execute()
->fetchField();
$this->assertNotFalse($go_db_id,
"Missing the 'GO' database record after loading the GO plant slim.");
}
/**
* Tests that an OBO from a local path can be loaded.
*
* For this test we will use a test ontology.
*
* @group obo
*/
public function testLocalOBO() {
$name = 'tripal_obo_test';
$path = __DIR__ . '/../example_files/test.obo';
$this->loadOBO($name, $path);
// Make sure we have a proper vocabulary record.
$tot_cv_id = db_select('chado.cv', 'c')
->fields('c', ['cv_id'])
->condition('name', 'tripal_obo_test')
->execute()
->fetchField();
$this->assertNotFalse($tot_cv_id,
"Missing the 'tripal_obo_test' cv record after loading the test.obo file");
// Make sure we have a proper database record.
$tot_db_id = db_select('chado.db', 'd')
->fields('d', ['db_id'])
->condition('name', 'TOT')
->execute()
->fetchField();
$this->assertNotFalse($tot_db_id,
"Missing the 'TOT' db record after loading the test.obo file");
return [[$tot_cv_id, $tot_db_id]];
}
/**
* Test that all nodes in our test OBO are loaded.
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testCVterms($cv_id, $db_id) {
// Our test OBO has 14 nodes.
$nodes = [
['TOT:001' => 'node01'],
['TOT:002' => 'node02'],
['TOT:003' => 'node03'],
['TOT:004' => 'node04'],
['TOT:005' => 'node05'],
['TOT:006' => 'node06'],
['TOT:007' => 'node07'],
['TOT:008' => 'node08'],
['TOT:009' => 'node09'],
['TOT:010' => 'node10'],
['TOT:011' => 'node11'],
['TOT:012' => 'node12'],
['TOT:013' => 'node13'],
['TOT:014' => 'node14'],
];
// Test that the proper records were added to identify the term.
foreach ($nodes as $id => $node_name) {
// Check that cvterm record is inserted.
$cvterm_id = db_select('chado.cvterm', 'cvt')
->fields('cvt', ['cvterm_id'])
->condition('cvt.name', $node_name)
->condition('cvt.cv_id', $cv_id)
->execute()
->fetchField();
$this->assertNotFalse($cvterm_id,
"Missing the cvterm record with name, '$node' after loading the test.obo file");
// Check that the dbxref record is inserted.
$accession = preg_replace('/TOT:/', '', $id);
$dbxref_id = db_select('chado.dbxref', 'dbx')
->fields('dbx', ['dbxref_id'])
->condition('accession', $accession)
->condition('db_id', $db_id);
$this->assertNotFalse($cvterm_id,
"Missing the dbxref record forid, '$id' after loading the test.obo file");
}
// Test node 11 to make sure the definition was inserted correctly.
// The definition for node11 has an extra colon and a comment. The colon
// should not throw off the insertion of the full definition and
// the comment should be excluded.
$def = db_select('chado.cvterm', 'cvt')
->fields('cvt', ['definition'])
->condition('cvt.name', 'node11')
->condition('cvt.cv_id', $cv_id)
->execute()
->fetchField();
$this->assertNotFalse($def,
"The definition for node11 was not added.");
$this->assertEquals('This is node 11 : Yo', $def,
"The definition for node11 is incorrect. it was stored as \"$def\" but should be \"def: This is node 11 : Yo\".");
// Make sure that colons in term names don't screw up the term. This test
// corresponds to the term with id CHEBI:132502 in the test.obo file.
$exists = db_select('chado.cv', 'c')
->fields('c', ['cv_id'])
->condition('name', 'fatty acid 18')
->execute()
->fetchField();
$this->assertFalse($exists);
// Node14 should be marked as obsolete.
$sql = "
SELECT CVT.is_obsolete
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} DB on DB.db_id = DBX.db_id
WHERE DB.name = 'TOT' and DBX.accession = '014'
";
$is_obsolete = chado_query($sql)->fetchField();
$this->assertEquals(1, $is_obsolete,
"The term, node14, should be marked as obsolete after loading of the test.obo file.");
// Every vocabulary should have an is_a term added to support the is_a
// relationships.
$sql = "
SELECT CVT.is_relationshiptype
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} DB on DB.db_id = DBX.db_id
WHERE CVT.name = 'is_a' and DB.name = 'TOT'
";
$is_reltype = chado_query($sql)->fetchField();
$this->assertNotFalse($is_reltype,
"The cvterm record for, is_a, should have been added during loading of the test.obo file.");
$this->assertEquals(1, $is_reltype,
"The cvterm record, is_a, should be marked as a relationship type.");
}
/**
* Test that insertion of synonyms works.
*
* The term 'node11' has a synonym:"crazy node" EXACT []
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testSynonyms($cv_id, $db_id) {
$query = db_select('chado.cvtermsynonym', 'cvts');
$query->fields('cvts', ['synonym']);
$query->join('chado.cvterm', 'cvt', 'cvts.cvterm_id = cvt.cvterm_id');
$query->condition('cvt.name', 'node11');
$synonym = $query->execute()->fetchField();
$this->assertNotFalse($synonym,
"Failed to find the 'crazy node' synonym record for node 11 after loading the test.obo file.");
$this->assertEquals("crazy node", $synonym,
"Failed to properly add the 'crazy node' synonym for node 11 instead the following was loaded: $synonym");
}
/**
* Test that insertion of subset works.
*
* The term 'node11' belongs to the test_crazy subset. Everything else belongs
* to the test_normal subset.
*
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testSubset($cv_id, $db_id) {
$sql = "
SELECT CVT.name
FROM {cvtermprop} CVTP
INNER JOIN {cvterm} CVTPT on CVTPT.cvterm_id = CVTP.type_id
INNER JOIN {cvterm} CVT on CVT.cvterm_id = CVTP.cvterm_id
INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
INNER JOIN {db} DB on DB.db_id = DBX.db_id
WHERE CVTPT.name = 'Subgroup' and DB.name = 'TOT' and CVTP.value = 'test_crazy'
";
$term_name = chado_query($sql)->fetchField();
$this->assertNotFalse($term_name,
"This cvtermprop record for the subset 'test_crazy' is missing.");
$this->assertEquals('node11', $term_name,
"This cvtermprop record for the subset 'test_crazy' is assigned to term, $term_name, instead of node11.");
$sql = "
SELECT count(CVT.cvterm_id)
FROM {cvtermprop} CVTP
INNER JOIN {cvterm} CVTPT on CVTPT.cvterm_id = CVTP.type_id
INNER JOIN {cvterm} CVT on CVT.cvterm_id = CVTP.cvterm_id
INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
INNER JOIN {db} DB on DB.db_id = DBX.db_id
WHERE CVTPT.name = 'Subgroup' and DB.name = 'TOT' and CVTP.value = 'test_normal'
";
$subset_count = chado_query($sql)->fetchField();
$this->assertNotFalse($subset_count,
"This cvtermprop record for the subset 'test_normal' are missing.");
// There should be 12 terms that belong to subset 'test_normal' as node14
// does not belong to a subset.
$this->assertEquals(12, $subset_count,
"There are $subset_count cvtermprop record for the subset 'test_normal' but there should be 13.");
}
/**
* Test that the insertion of xref works.
*
* The term 'node11' belongs to the test_crazy subset. Everything else belongs
* to the test_normal subset.
*
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testXref($cv_id, $db_id) {
$sql = "
SELECT concat(DB2.name, ':', DBX2.accession)
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} on DB.db_id = DBX.db_id
INNER JOIN {cvterm_dbxref} CVTDBX on CVTDBX.cvterm_id = CVT.cvterm_id
INNER JOIN {dbxref} DBX2 on DBX2.dbxref_id = CVTDBX.dbxref_id
INNER JOIN {db} DB2 on DB2.db_id = DBX2.db_id
WHERE DB.name = 'TOT' and CVT.name = 'node11'
ORDER BY DBX.accession
";
$xref_id = chado_query($sql)->fetchField();
$this->assertNotFalse($xref_id,
"This cvterm_dbxref record for the xref 'GO:0043226' is missing for node11.");
$this->assertEquals('GO:0043226', $xref_id,
"This cvterm_dbxref record for node 11 is, $xref_id, instead of GO:0043226.");
}
/**
* Test that the insertion of comments works.
*
* The term 'node11' contains a comment.
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testComment($cv_id, $db_id) {
$sql = "
SELECT CVTP.value
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} on DB.db_id = DBX.db_id
INNER JOIN {cvtermprop} CVTP on CVTP.cvterm_id = CVT.cvterm_id
INNER JOIN {cvterm} CVTPT on CVTPT.cvterm_id = CVTP.type_id
WHERE DB.name = 'TOT' and CVTPT.name = 'comment' and CVT.name = 'node11'
ORDER BY DBX.accession
";
$comment = chado_query($sql)->fetchField();
$this->assertNotFalse($xref_id,
"This cvterm_dbxref record for the xref 'This is a crazy node' is missing for node11.");
$this->assertEquals('This is a crazy node', $comment,
"This cvterm_dbxref record for node11 is, \"$comment\", instead of \"This is a crazy node\".");
}
/**
* Tests that the cvtermpath is properly loaded.
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testRelationships($cv_id, $db_id) {
$relationships = [
['node02', 'is_a', 'node01'],
['node03', 'is_a', 'node01'],
['node04', 'is_a', 'node01'],
['node04', 'has_part', 'node11'],
['node05', 'is_a', 'node01'],
['node06', 'is_a', 'node03'],
['node07', 'is_a', 'node03'],
['node08', 'is_a', 'node07'],
['node09', 'is_a', 'node04'],
['node09', 'is_a', 'node07'],
['node10', 'is_a', 'node05'],
['node11', 'is_a', 'node09'],
['node11', 'is_a', 'node10'],
['node12', 'is_a', 'node10'],
['node13', 'is_a', 'node11'],
];
foreach ($relationships as $relationship) {
$subject = $relationship[0];
$type = $relationship[1];
$object = $relationship[2];
$sql = "
SELECT CVTR.cvterm_relationship_id
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} on DB.db_id = DBX.db_id
INNER JOIN {cvterm_relationship} CVTR on CVTR.subject_id = CVT.cvterm_id
INNER JOIN {cvterm} CVT2 on CVT2.cvterm_id = CVTR.object_id
INNER JOIN {cvterm} CVT3 on CVT3.cvterm_id = CVTR.type_id
WHERE DB.name = 'TOT' AND CVT2.name = :object AND
CVT3.name = :type AND CVT.name = :subject
";
$args = [':object' => $object, ':type' => $type, ':subject' => $subject];
$rel_id = chado_query($sql, $args)->fetchField();
$this->assertNotFalse($rel_id,
"The following relationship could not be found: $subect $type $object.");
}
// Now make sure we have no more relationships than what we are supposed
// to have.
$sql = "
SELECT count(CVTR.cvterm_relationship_id)
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} on DB.db_id = DBX.db_id
INNER JOIN {cvterm_relationship} CVTR on CVTR.object_id = CVT.cvterm_id
WHERE DB.name = 'TOT' AND CVT.is_relationshiptype = 0
";
$rel_count = chado_query($sql)->fetchField();
$expected = count($relationships);
$this->assertEquals($expected, $rel_count,
"There are an incorrect number of relationships. There were $rel_count found but there should be $expected.");
}
/**
* Tests that the cvtermpath is properly loaded.
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testCVtermPath($cv_id, $db_id) {
// For now we won't include distance or type in the check because depending
// how the tree was loaded and if there are multiple paths to a node
// then there's no guarantee we'll always get the same path. Therefore the
// type and pathdistance may be different (althoug not incorrect).
$relationships = [
// Node01 as root: note that the root term always has a link to itself
// in the cvtermpath table.
['node01', 'node01'],
['node01', 'node02'],
['node01', 'node03'],
['node01', 'node04'],
['node01', 'node05'],
['node01', 'node06'],
['node01', 'node07'],
['node01', 'node08'],
['node01', 'node09'],
['node01', 'node10'],
['node01', 'node11'],
['node01', 'node12'],
['node01', 'node13'],
// Node03 as root.
['node03', 'node04'],
['node03', 'node06'],
['node03', 'node07'],
['node03', 'node08'],
['node03', 'node09'],
['node03', 'node11'],
['node03', 'node13'],
// Node04 as root.
['node04', 'node09'],
['node04', 'node11'],
['node04', 'node13'],
// Node05 as root.
['node05', 'node04'],
['node05', 'node09'],
['node05', 'node10'],
['node05', 'node11'],
['node05', 'node12'],
['node05', 'node13'],
// Node07 as root.
['node07', 'node04'],
['node07', 'node08'],
['node07', 'node09'],
['node07', 'node11'],
['node07', 'node13'],
// Node09 as root.
['node09', 'node04'],
['node09', 'node11'],
['node09', 'node13'],
// Node10 as root.
['node10', 'node04'],
['node10', 'node09'],
['node10', 'node11'],
['node10', 'node12'],
['node10', 'node13'],
// Node11 as root.
['node11', 'node04'],
['node11', 'node09'],
['node11', 'node13'],
];
// Populate the cvtermpath for our test OBO.
chado_update_cvtermpath($cv_id);
foreach ($relationships as $relationship) {
$object = $relationship[0];
$subject = $relationship[1];
$sql = "
SELECT cvtermpath_id
FROM {cvtermpath} CVTP
INNER JOIN {cvterm} CVTO on CVTO.cvterm_id = CVTP.object_id
INNER JOIN {cvterm} CVTS on CVTS.cvterm_id = CVTP.subject_id
INNER JOIN {cvterm} CVTT on CVTT.cvterm_id = CVTP.type_id
WHERE CVTP.cv_id = :cv_id and CVTO.name = :object and
CVTS.name = :subject
";
$args = [
':cv_id' => $cv_id,
':object' => $object,
':subject' => $subject,
];
$cvtermpath_id = chado_query($sql, $args)->fetchField();
$this->assertNotFalse($cvtermpath_id,
"Cound not find the cvtermpath record for the relationship: $subject => $object.");
}
// Now make sure we have no additional entries.
$sql = "
SELECT count(cvtermpath_id)
FROM {cvtermpath} CVTP
INNER JOIN {cvterm} CVTO on CVTO.cvterm_id = CVTP.object_id
INNER JOIN {cvterm} CVTS on CVTS.cvterm_id = CVTP.subject_id
INNER JOIN {cvterm} CVTT on CVTT.cvterm_id = CVTP.type_id
WHERE CVTP.cv_id = :cv_id
";
$args = [':cv_id' => $cv_id];
$rel_count = chado_query($sql, $args)->fetchField();
$expected = count($relationships);
$this->assertEquals($expected, $rel_count,
"There are an incorrect number of paths. There were $rel_count found but there should be $expected.");
}
/**
* Tests that the EBI Lookup is properly working.
*
* The term CHEBI:132502 should have been loaded via EBI.
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testEBILookup($cv_id, $db_id) {
$sql = "
SELECT CVT.cvterm_id
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} DB on DB.db_id = DBX.db_id
WHERE DB.name = 'CHEBI' and DBX.accession = '132502'
";
$cvterm_id = chado_query($sql)->fetchField();
$this->assertNotFalse($cvterm_id,
"The term, CHEBI:132502, is not present the EBI OLS lookup must not have succeeded.");
}
/**
* Tests when changes are made between OBO loads.
*
* Sometimes an ontology can change the names of it's terms, or set some
* as obsolete, etc. We need to makes sure that when changes are made and
* the OBO is reloaded that the terms are properly update.
*
* @group obo
* @dataProvider testLocalOBO
*/
public function testOBOChanges($cv_id, $db_id) {
$name = 'tripal_obo_test_update';
$path = __DIR__ . '/../example_files/test.update.obo';
$this->loadOBO($name, $path);
// Did the name of term 13 change?
$sql = "
SELECT CVT.name
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} DB on DB.db_id = DBX.db_id
WHERE DB.name = 'TOT' and DBX.accession = '013'
";
$name = chado_query($sql)->fetchField();
$this->assertEquals('New name 13.', $name,
"The name for node13 (TOT:013) failed to update to 'New name 13'.");
// Node15 is new, and node02 got removed. Node15 now uses node02's name and
// has TOT:002 as an alt_id. So, node02 should be marked as obsolete
$sql = "
SELECT CVT.is_obsolete
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} DB on DB.db_id = DBX.db_id
WHERE DB.name = 'TOT' and DBX.accession = '002'
";
$is_obsolete = chado_query($sql)->fetchField();
$this->assertEquals(1, $is_obsolete,
"The node02 (TOT:002) should be marked as obsolete after update.");
// Node16 is new, and node08 is now obsolete. Node16 now uses node08's name,
// so, node08 should be marked as obsolete and have the word '(obsolete)'
// added to prevent future conflicts.
$sql = "
SELECT CVT.name
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN {db} DB on DB.db_id = DBX.db_id
WHERE DB.name = 'TOT' and DBX.accession = '008'
";
$name = chado_query($sql)->fetchField();
$this->assertEquals("node08 (obsolete)", $name,
"The node08 (TOT:008) should be marked as obsolete after update.");
}
/**
* @group obo
* @group chado
*/
public function testfindEBITerm_finder_retrieves_term() {
module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/OBOImporter');
$importer_private = new \OBOImporter();
$importer = reflect($importer_private);
$id = 'PECO:0007085';
$result = $importer->findEBITerm($id);
$this->assertNotEmpty($result);
$this->assertEquals('fertilizer exposure', $result['name'][0]);
}
}