From 33b621a67e1dedd416929797f635d81f66169ff3 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 5 Aug 2013 14:07:01 +0000
Subject: [PATCH] updated to use patch database rather than old core also some
 ergonomical changes: - get a count+ is test replaced by is_count method -
 variable names declared at the top of the modules, so can easily change
 gene/dbid/db used if the test database changes

---
 modules/t/attributeAdaptor.t | 170 +++++++++++++++++++----------------
 1 file changed, 92 insertions(+), 78 deletions(-)

diff --git a/modules/t/attributeAdaptor.t b/modules/t/attributeAdaptor.t
index cadf6148bd..84d9ef7994 100644
--- a/modules/t/attributeAdaptor.t
+++ b/modules/t/attributeAdaptor.t
@@ -11,9 +11,14 @@ our $verbose = 1;
 our $clean   = 0;
 
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new;
+my $dbtype = 'patch';
+my $dbid = 92975;
+my $stable_id = "ENSG00000112761";
+my $stable_id2 = "ENSG00000112769";
+my $count;
 
-# get a core DBAdaptor
-my $db = $multi->get_DBAdaptor("core");
+# get a DBAdaptor
+my $db = $multi->get_DBAdaptor($dbtype);
 
 my $slice_adaptor = $db->get_SliceAdaptor();
 my $mfa           = $db->get_MiscFeatureAdaptor();
@@ -24,61 +29,58 @@ my $ga            = $db->get_GeneAdaptor();
 #
 my $aa = $db->get_AttributeAdaptor();
 
-ok($aa && ref($aa) && $aa->isa('Bio::EnsEMBL::DBSQL::AttributeAdaptor'));
+is(ref($aa), 'Bio::EnsEMBL::DBSQL::AttributeAdaptor', "We have an attribute adaptor");
 
 # hide the contents of the attrib_type, misc_attrib, seq_region_attrib tables
 # so we can test storing etc. with a clean slate
-$multi->hide('core', 'misc_attrib', 'seq_region_attrib', 'attrib_type', 'gene_attrib');
+$multi->hide($dbtype, 'misc_attrib', 'seq_region_attrib', 'attrib_type', 'gene_attrib');
 
 ##############
 # MiscFeature functionality tests
 #
 
 my $attrib = Bio::EnsEMBL::Attribute->new(-NAME        => 'test_name',
-										  -CODE        => 'test_code',
-										  -DESCRIPTION => 'test_desc',
-										  -VALUE       => 'test_value');
+				          -CODE        => 'test_code',
+					  -DESCRIPTION => 'test_desc',
+					  -VALUE       => 'test_value');
 
-my $mf = $mfa->fetch_by_dbID(1);
+my $mf = $mfa->fetch_by_dbID($dbid);
 $aa->store_on_MiscFeature($mf, [$attrib]);
 
 #
 # make sure the misc_attrib table was updated
 #
-my $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM misc_attrib " . "WHERE misc_feature_id = 1")->[0]->[0];
-
-ok($count == 1);
+is_rows(1, $db, "misc_attrib", "where misc_feature_id = ? ", [$dbid]);
 
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code'")->[0]->[0];
-ok($count == 1);
+is_rows(1, $db, "attrib_type", "where code = ? ", ["test_code"]);
 
 #
 # test that we can now retrieve this attribute
 #
 my @attribs = @{$aa->fetch_all_by_MiscFeature($mf)};
 
-ok(@attribs == 1);
+is(@attribs, 1, "Fetched 1 features");
 
 $attrib = $attribs[0];
 
-ok($attrib->name        eq 'test_name');
-ok($attrib->code        eq 'test_code');
-ok($attrib->description eq 'test_desc');
-ok($attrib->value       eq 'test_value');
+is($attrib->name, 'test_name', "Attrib name is test_name");
+is($attrib->code, 'test_code', "Attrib code is test_code");
+is($attrib->description, 'test_desc', "Attrib description is test_desc");
+is($attrib->value, 'test_value', "Attrib value is test_value");
 
 @attribs = @{$aa->fetch_all_by_MiscFeature()};
 
-ok(@attribs == 1);
+is(@attribs, 1, "One attrib fetched");
 
 $attrib = $attribs[0];
 
-ok($attrib->name        eq 'test_name');
-ok($attrib->code        eq 'test_code');
-ok($attrib->description eq 'test_desc');
-ok($attrib->value       eq 'test_value');
+is($attrib->name, 'test_name', "Attrib name is test_name");
+is($attrib->code, 'test_code', "Attrib code is test_code");
+is($attrib->description, 'test_desc', "Attrib description is test_desc");
+is($attrib->value, 'test_value', "Attrib value is test_value");
 
 #
 # test the removal of this attribute
@@ -88,15 +90,14 @@ $aa->remove_from_MiscFeature($mf);
 #
 # make sure the misc_attrib table was updated
 #
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM misc_attrib " . "WHERE misc_feature_id = 1")->[0]->[0];
 
-ok($count == 0);
+is_rows(0, $db, "misc_attrib", "where misc_feature_id = ? ", [$dbid]);
 
 #
 # make sure the attribute is no longer retrievable
 #
 @attribs = @{$aa->fetch_all_by_MiscFeature($mf)};
-ok(@attribs == 0);
+is(@attribs, 0, "Attribute is no longer retrievable");
 
 #################
 # Slice functionality tests
@@ -107,67 +108,64 @@ $attrib = Bio::EnsEMBL::Attribute->new(-NAME        => 'test_name2',
 									   -DESCRIPTION => 'test_desc2',
 									   -VALUE       => 'test_value2');
 
-my $slice = $slice_adaptor->fetch_by_region('chromosome', '20');
+my $slice = $slice_adaptor->fetch_by_region('chromosome', '6');
 
 $aa->store_on_Slice($slice, [$attrib]);
+my $seqid = $slice->get_seq_region_id();
 
 #
 # make sure the seq_region_attrib table was updated
 #
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
 
-ok($count == 1);
+is_rows(1, $db, "seq_region_attrib", "where seq_region_id = ? ", [$seqid]);
 
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0];
-ok($count == 1);
+is_rows(1, $db, "attrib_type", "where code = ? ", ["test_code2"]);
 
 #
 # test that we can now retrieve this attribute
 #
 @attribs = @{$aa->fetch_all_by_Slice($slice)};
-ok(@attribs == 1);
+is(@attribs, 1, "Fetched attribute");
 
 @attribs = @{$aa->fetch_all_by_Slice($slice, "rubbish")};
-ok(@attribs == 0);
+is(@attribs, 0, "No attribute fetched for code rubbish");
 
 @attribs = @{$aa->fetch_all_by_Slice($slice, "test_code2")};
-ok(@attribs == 1);
+is(@attribs, 1, "One attribute fetched for test_code2");
 
 @attribs = @{$aa->fetch_all_by_Slice(undef, "test_code2")};
-ok(@attribs == 1);
+is(@attribs, 1, "One attribute fetched across all slices");
 
 $attrib = $attribs[0];
 
-ok($attrib->name        eq 'test_name2');
-ok($attrib->code        eq 'test_code2');
-ok($attrib->description eq 'test_desc2');
-ok($attrib->value       eq 'test_value2');
+is($attrib->name, 'test_name2', "Attrib name is test_name2");
+is($attrib->code, 'test_code2', "Attrib code is test_code2");
+is($attrib->description, 'test_desc2', "Attrib description is test_desc2");
+is($attrib->value, 'test_value2', "Attrib value is test_value2");
 
 #
-# test the removal of this attribute with atrrib code
+# test the removal of this attribute with attrib code
 #
 $aa->remove_from_Slice($slice, "junk");
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
 
-ok($count == 1);
+is_rows(1, $db, "seq_region_attrib", "where seq_region_id = ? ", [$seqid]);
 
 #
 # test the removal of this attribute
 #
 
 $aa->remove_from_Slice($slice, "test_code2");
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
 
-ok($count == 0);
+is_rows(0, $db, "seq_region_attrib", "where seq_region_id = ? ", [$seqid]);
 
 #
 # make sure the attribute is no longer retrievable
 #
 @attribs = @{$aa->fetch_all_by_Slice($slice)};
-ok(@attribs == 0);
+is(@attribs, 0, "No attribs left for slice");
 
 #
 # try to add an attribute with an already existing code
@@ -176,30 +174,26 @@ $aa->store_on_Slice($slice, [$attrib]);
 #
 # make sure the seq_region_attrib table was updated
 #
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
 
-ok($count == 1);
+is_rows(1, $db, "seq_region_attrib", "where seq_region_id = ? ", [$seqid]);
 
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0];
-ok($count == 1);
+is_rows(1, $db, "attrib_type", "where code = ? ", ["test_code2"]);
 
 @attribs = @{$aa->fetch_all_by_Slice($slice)};
-note "attribs: " . scalar(@attribs);
-ok(@attribs == 1);
+is(@attribs, 1, "One attrib on slice");
 
 @attribs = @{$aa->fetch_all_by_Slice(undef)};
-ok(@attribs == 1);
+is(@attribs, 1, "One attrib for all slices");
 
 #
 # test the removal of this attribute
 #
 $aa->remove_from_Slice($slice);
-$count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
 
-ok($count == 0);
+is_rows(0, $db, "seq_region_attrib", "where seq_region_id = ? " , [$seqid]);
 
 #
 # test the storage of empty attrib values
@@ -212,6 +206,12 @@ ok($count == 0);
   $aa->store_on_Slice($slice, [Bio::EnsEMBL::Attribute->new(%args, -VALUE => 0)]);
   my $new_rows = count_rows($db, 'seq_region_attrib');
   cmp_ok($new_rows, '>', $current_rows, 'Asserting the storage of undefined attributes will always store them');
+  # now remove again
+  $aa->remove_from_Slice($slice);
+  $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM seq_region_attrib " . "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
+
+  is_rows(0, $db, "seq_region_attrib", "where seq_region_id = ? ", [$seqid]);
+
 }
 
 #################
@@ -223,7 +223,7 @@ $attrib = Bio::EnsEMBL::Attribute->new(-NAME        => 'test_name2',
 									   -DESCRIPTION => 'test_desc2',
 									   -VALUE       => 'test_value2');
 
-my $gene = $ga->fetch_by_stable_id('ENSG00000171456');
+my $gene = $ga->fetch_by_stable_id($stable_id);
 
 $aa->store_on_Gene($gene, [$attrib]);
 
@@ -232,35 +232,35 @@ $aa->store_on_Gene($gene, [$attrib]);
 #
 $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
 
-ok($count == 1);
+is($count, 1, "One gene attrib fetched");
 
 #
 # make sure the attrib_type table was updated
 #
 $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0];
-ok($count == 1);
+is($count, 1, "One attrib_type available");
 
 #
 # test that we can now retrieve this attribute
 #
 @attribs = @{$aa->fetch_all_by_Gene($gene)};
-ok(@attribs == 1);
+is(@attribs, 1, "Fetched one attribute for gene");
 
 @attribs = @{$aa->fetch_all_by_Gene($gene, "rubbish")};
-ok(@attribs == 0);
+is(@attribs, 0, "Fetched no attribute for code rubbish");
 
 @attribs = @{$aa->fetch_all_by_Gene($gene, "test_code2")};
-ok(@attribs == 1);
+is(@attribs, 1, "Fetched one attribute for code test_code2");
 
 @attribs = @{$aa->fetch_all_by_Gene(undef, "test_code2")};
-ok(@attribs == 1);
+is(@attribs, 1, "Fetch one attribute for genes");
 
 $attrib = $attribs[0];
 
-ok($attrib->name        eq 'test_name2');
-ok($attrib->code        eq 'test_code2');
-ok($attrib->description eq 'test_desc2');
-ok($attrib->value       eq 'test_value2');
+is($attrib->name, 'test_name2', "Attrib name is test_name2");
+is($attrib->code, 'test_code2', "Attrib code is test_code2");
+is($attrib->description, 'test_desc2', "Attrib description is test_desc2");
+is($attrib->value, 'test_value2', "Attrib value is test_value2");
 
 #
 # test the removal of this attribute with atrrib code
@@ -268,7 +268,7 @@ ok($attrib->value       eq 'test_value2');
 $aa->remove_from_Gene($gene, "junk");
 $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
 
-ok($count == 1);
+is($count, 1, "One gene attrib available");
 
 #
 # test the removal of this attribute
@@ -277,13 +277,13 @@ ok($count == 1);
 $aa->remove_from_Gene($gene, "test_code2");
 $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
 
-ok($count == 0);
+is($count, 0, "Gene attrib has been removed");
 
 #
 # make sure the attribute is no longer retrievable
 #
 @attribs = @{$aa->fetch_all_by_Gene($gene)};
-ok(@attribs == 0);
+is(@attribs, 0, "No attribs available for gene");
 
 #
 # try to add an attribute with an already existing code
@@ -294,20 +294,20 @@ $aa->store_on_Gene($gene, [$attrib]);
 #
 $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
 
-ok($count == 1);
+is($count, 1, "One attrib added for gene");
 
 #
 # make sure the attrib_type table was updated
 #
 $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM attrib_type " . "WHERE code = 'test_code2'")->[0]->[0];
-ok($count == 1);
+is($count, 1, "One attrib stored for code test_code2");
 
 @attribs = @{$aa->fetch_all_by_Gene($gene)};
 note "attribs: " . scalar(@attribs);
-ok(@attribs == 1);
+is(@attribs, 1, "One attrib for gene");
 
 @attribs = @{$aa->fetch_all_by_Gene(undef)};
-ok(@attribs == 1);
+is(@attribs, 1, "One attrib for genes");
 
 #
 # test the removal of this attribute
@@ -315,7 +315,7 @@ ok(@attribs == 1);
 $aa->remove_from_Gene($gene);
 $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
 
-ok($count == 0);
+is($count, 0, "Attrib has been removed from gene");
 
 #
 # test the storage of empty attrib values
@@ -332,7 +332,7 @@ ok($count == 0);
   $aa->remove_from_Gene($gene);
   $count = $db->dbc->db_handle->selectall_arrayref("SELECT count(*) FROM gene_attrib " . "WHERE gene_id = " . $gene->dbID())->[0]->[0];
 
-  ok($count == 0);
+  is($count, 0, "Attrib has been removed from gene");
 
 }
 
@@ -340,7 +340,7 @@ ok($count == 0);
 # Test batch storage
 #
 
-my $gene2 = $ga->fetch_by_stable_id('ENSG00000131044');
+my $gene2 = $ga->fetch_by_stable_id($stable_id2);
 my $batch = {$gene->dbID()  => [Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2', -CODE => 'test_code2', -DESCRIPTION => 'test_desc2', VALUE => 'val1'), Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2', -CODE => 'test_code2', -DESCRIPTION => 'test_desc2', VALUE => 'val2')],
 			 $gene2->dbID() => [Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2', -CODE => 'test_code2', -DESCRIPTION => 'test_desc2', VALUE => 'val3'),]};
 my $current_rows = count_rows($db, 'gene_attrib');
@@ -349,11 +349,25 @@ my $new_rows = count_rows($db, 'gene_attrib');
 cmp_ok($new_rows, '=', $current_rows + 3, 'Asserting the storage of multiple attributes will always store them');
 
 @attribs = @{$aa->fetch_all_by_Gene($gene)};
-ok(@attribs == 2);
+is(@attribs, 2, "Two attribs available for gene");
 
 @attribs = @{$aa->fetch_all_by_Gene($gene2)};
-ok(@attribs == 1);
+is(@attribs, 1, "One attrib stored for gene2");
+
+my $slice2 = $slice_adaptor->fetch_by_region('chromosome', 'X');
+my $batch = {$slice->get_seq_region_id()  => [Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2', -CODE => 'test_code2', -DESCRIPTION => 'test_desc2', VALUE => 'val1'), Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2', -CODE => 'test_code2', -DESCRIPTION => 'test_desc2', VALUE => 'val2')],
+                         $slice2->get_seq_region_id() => [Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2', -CODE => 'test_code2', -DESCRIPTION => 'test_desc2', VALUE => 'val3'),]};
+my $current_rows = count_rows($db, 'seq_region_attrib');
+$aa->store_batch_on_Slice($batch);
+my $new_rows = count_rows($db, 'seq_region_attrib');
+cmp_ok($new_rows, '=', $current_rows + 3, 'Asserting the storage of multiple attributes will always store them');
+
+@attribs = @{$aa->fetch_all_by_Slice($slice)};
+is(@attribs, 2, "Two attribs available for slice");
+
+@attribs = @{$aa->fetch_all_by_Slice($slice2)};
+is(@attribs, 1, "One attrib stored for slice2");
 
-$multi->restore('core', 'misc_attrib', 'seq_region_attrib', 'attrib_type');
+$multi->restore($dbtype, 'misc_attrib', 'seq_region_attrib', 'attrib_type');
 
 done_testing();
-- 
GitLab