Commit 22d947c7 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

added tests on stable id event for a given archive stable id and stable id

also updated existing tests to use is rather than ok whenever possible
parent 7c3f4dec
...@@ -27,13 +27,13 @@ my $asia = $db->get_ArchiveStableIdAdaptor(); ...@@ -27,13 +27,13 @@ my $asia = $db->get_ArchiveStableIdAdaptor();
# 2-4 ArchiveStableId retrieval # 2-4 ArchiveStableId retrieval
# #
my $asi = $asia->fetch_by_stable_id("T1"); my $asi = $asia->fetch_by_stable_id("T1");
ok( $asi->release == 2); is( $asi->release, 2, "T1 is from release 2");
$asi = $asia->fetch_by_stable_id_version("T2", 3); $asi = $asia->fetch_by_stable_id_version("T2", 3);
ok( $asi->release == 3); is( $asi->release, 3, "T2 is from release 3");
$asi = $asia->fetch_by_stable_id_dbname("T1", "release_2"); $asi = $asia->fetch_by_stable_id_dbname("T1", "release_2");
ok( $asi->release == 2); is( $asi->release, 2, "T1 is from release 2");
# #
...@@ -46,10 +46,36 @@ ok( $asi ); ...@@ -46,10 +46,36 @@ ok( $asi );
# #
# 6 how many predecessors does it have # 6 retrieval of the event related to a specific stable id
#
my $event = $asi->get_event("G2");
is(ref($event), 'Bio::EnsEMBL::StableIdEvent', "A stable id event was fetched");
is($event->score, 0.54, "Mapping score between G1 and G2");
my $old_archive_stable_id = $event->old_ArchiveStableId;
my $new_archive_stable_id = $event->new_ArchiveStableId;
is($new_archive_stable_id, $asi, "Initial archive is new archive");
is($old_archive_stable_id->stable_id, "G2", "Old stable id");
is($new_archive_stable_id->stable_id, "G1", "New stable id");
$event = $old_archive_stable_id->get_event("G1");
is($event->score, 0.54, "Mapping score between G1 and G2");
$old_archive_stable_id = $event->old_ArchiveStableId;
$new_archive_stable_id = $event->new_ArchiveStableId;
is($old_archive_stable_id->stable_id, "G2", "Old stable id");
is($new_archive_stable_id->stable_id, "G1", "New stable id");
#
# 7 how many predecessors does it have
# #
my $pre_asis = $asi->get_all_predecessors(); my $pre_asis = $asi->get_all_predecessors();
ok( scalar( @$pre_asis ) == 2 ); is( scalar( @$pre_asis ), 2, "G1 has 2 predecessors" );
for my $asi ( @$pre_asis ) { for my $asi ( @$pre_asis ) {
debug( "\tPre G1" ); debug( "\tPre G1" );
...@@ -58,7 +84,7 @@ for my $asi ( @$pre_asis ) { ...@@ -58,7 +84,7 @@ for my $asi ( @$pre_asis ) {
# #
# 7 transcripts for a gene # 8 transcripts for a gene
# #
my $transcripts = $pre_asis->[0]->get_all_transcript_archive_ids(); my $transcripts = $pre_asis->[0]->get_all_transcript_archive_ids();
...@@ -72,20 +98,20 @@ for my $asi ( @$transcripts ) { ...@@ -72,20 +98,20 @@ for my $asi ( @$transcripts ) {
} }
} }
ok( scalar( @$transcripts ) == 1); is( scalar( @$transcripts ), 1, "G1 has 1 transcript");
# #
# 8 no predecessor case # 9 no predecessor case
# #
$pre_asis = $pre_asis->[0]->get_all_predecessors(); $pre_asis = $pre_asis->[0]->get_all_predecessors();
debug( "\tPredecessors: ".scalar( @$pre_asis ) ); debug( "\tPredecessors: ".scalar( @$pre_asis ) );
ok( scalar( @$pre_asis ) == 0 ); is( scalar( @$pre_asis ), 0, "No predecessors found" );
# #
# 9 successor case # 10 successor case
# #
$asi = $asia->fetch_by_stable_id_dbname( "G4", "release_1" ); $asi = $asia->fetch_by_stable_id_dbname( "G4", "release_1" );
my $succ_asis = $asi->get_all_successors(); my $succ_asis = $asi->get_all_successors();
...@@ -95,10 +121,10 @@ for my $asi ( @$succ_asis ) { ...@@ -95,10 +121,10 @@ for my $asi ( @$succ_asis ) {
_print_asi( $asi ); _print_asi( $asi );
} }
ok( scalar( @$succ_asis ) == 1 ); is( scalar( @$succ_asis ), 1, "G4 has 1 sucessor" );
# #
# 10 no successor case # 11 no successor case
# #
$succ_asis = $succ_asis->[0]->get_all_successors(); $succ_asis = $succ_asis->[0]->get_all_successors();
...@@ -107,11 +133,11 @@ for my $asi ( @$succ_asis ) { ...@@ -107,11 +133,11 @@ for my $asi ( @$succ_asis ) {
_print_asi( $asi ); _print_asi( $asi );
} }
ok( scalar( @$succ_asis ) == 0 ); is( scalar( @$succ_asis ), 0, "G4.1 has no sucessors");
# #
# 11 fetch_successor_history # 12 fetch_successor_history
# #
$asi = $asia->fetch_by_stable_id_dbname( "G2", "release_1" ); $asi = $asia->fetch_by_stable_id_dbname( "G2", "release_1" );
my $asis = $asia->fetch_successor_history( $asi ); my $asis = $asia->fetch_successor_history( $asi );
...@@ -121,30 +147,30 @@ for my $asi ( @$asis ) { ...@@ -121,30 +147,30 @@ for my $asi ( @$asis ) {
_print_asi( $asi ); _print_asi( $asi );
} }
ok(( $asis->[-1]->db_name eq "release_4" ) && is( $asis->[-1]->db_name, "release_4", "Current release for G2 is release 4");
( scalar @$asis == 5 )); is( scalar @$asis, 5, "G2 has 5 sucessors");
# #
# 12-16 history tree # 13-17 history tree
# #
$asi = $asia->fetch_by_stable_id_dbname( "G2", "release_1" ); $asi = $asia->fetch_by_stable_id_dbname( "G2", "release_1" );
my $history = $asi->get_history_tree; my $history = $asi->get_history_tree;
my @asis = @{ $history->get_all_ArchiveStableIds }; my @asis = @{ $history->get_all_ArchiveStableIds };
ok( scalar(@asis) == 9); is( scalar(@asis), 9, "G2 history has 9 related archives");
my @events = @{ $history->get_all_StableIdEvents }; my @events = @{ $history->get_all_StableIdEvents };
ok( scalar(@events) == 10); is( scalar(@events), 10, "G2 history has 10 related events");
ok( scalar(@{ $history->get_release_display_names }) == 4); is( scalar(@{ $history->get_release_display_names }), 4, "G2 has 4 display names");
ok( scalar(@{ $history->get_unique_stable_ids }) == 3); is( scalar(@{ $history->get_unique_stable_ids }), 3, "G2 has 3 unique stable ids");
my ($x, $y) = @{ $history->coords_by_ArchiveStableId($asi) }; my ($x, $y) = @{ $history->coords_by_ArchiveStableId($asi) };
ok( $x == 0 and $y == 1 ); ok( $x == 0 and $y == 1 );
# #
# 17-18 check for current version and fetch latest incarnation # 18-19 check for current version and fetch latest incarnation
# #
ok( ! $asi->is_latest, 'Not on the latest version so is_latest is false'); ok( ! $asi->is_latest, 'Not on the latest version so is_latest is false');
...@@ -153,7 +179,7 @@ ok($asi->is_latest(), 'Latest incarnation must be the latest version'); ...@@ -153,7 +179,7 @@ ok($asi->is_latest(), 'Latest incarnation must be the latest version');
is($asi->version, 4, 'Latest version is 4'); is($asi->version, 4, 'Latest version is 4');
# #
# 19 associated IDs in archive # 20 associated IDs in archive
# #
$asi = $asia->fetch_by_stable_id_version( "G2", "2" ); $asi = $asia->fetch_by_stable_id_version( "G2", "2" );
my @assoc = @{ $asi->get_all_associated_archived }; my @assoc = @{ $asi->get_all_associated_archived };
...@@ -166,7 +192,7 @@ ok( scalar(@assoc) == 2 and ...@@ -166,7 +192,7 @@ ok( scalar(@assoc) == 2 and
# #
# 20 archived peptide sequence # 21 archived peptide sequence
# #
$asi = $asia->fetch_by_stable_id_version("P2", 1); $asi = $asia->fetch_by_stable_id_version("P2", 1);
ok( $asi->get_peptide eq 'PTWOVERSIONONE*' ); ok( $asi->get_peptide eq 'PTWOVERSIONONE*' );
......
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