From e5323ff97f489e4da771a97e40a907d3871f2577 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@illinois.edu>
Date: Sat, 28 Feb 2015 16:57:49 -0600
Subject: [PATCH] tests (carried over from RemoteDB/Taxonomy.t so has some
 cruft)

---
 t/LocalDB/Taxonomy/sqlite.t | 247 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 247 insertions(+)
 create mode 100644 t/LocalDB/Taxonomy/sqlite.t

diff --git a/t/LocalDB/Taxonomy/sqlite.t b/t/LocalDB/Taxonomy/sqlite.t
new file mode 100644
index 000000000..2dc073bd0
--- /dev/null
+++ b/t/LocalDB/Taxonomy/sqlite.t
@@ -0,0 +1,247 @@
+# -*-Perl-*- Test Harness script for Bioperl
+# $Id$
+
+use strict;
+
+BEGIN {
+    use lib '.';
+    use Bio::Root::Test;
+
+    #test_begin(
+    #    
+    #    -requires_modules => [qw(DBI DBD::SQLite )]
+    #);
+
+    use_ok('Bio::DB::Taxonomy');
+    use_ok('Bio::Tree::Tree');
+}
+
+my $temp_dir = test_output_dir();
+
+ok my $db_flatfile = Bio::DB::Taxonomy->new(
+    -source    => 'sqlite',
+    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
+    -namesfile => test_input_file('taxdump', 'names.dmp'),
+    
+);
+isa_ok $db_flatfile, 'Bio::DB::Taxonomy::sqlite';
+isa_ok $db_flatfile, 'Bio::DB::Taxonomy';
+
+# By not specifying a '-directory' argument, index files go to a temporary
+# folder ($Bio::Root::IO::TEMPDIR, such as 'C:\Users\USER\AppData\Local\Temp'),
+# and are implied to be temporary. So test the ability of flatfile->DESTROY to
+# remove the temporary index files at object destruction (this also affects files
+# in "test_output_dir()", since the folder is created inside the temporary folder)
+no warnings qw(once); # silence 'Name "$Bio::Root::IO::TEMPDIR" used only once'
+
+is $db_flatfile->{index_directory}, $Bio::Root::IO::TEMPDIR, 'removal of temporary index files: no -directory';
+
+#$db_flatfile->DESTROY;
+#ok not -e ($db_flatfile->{index_directory} . '/id2names');
+#ok not -e ($db_flatfile->{index_directory} . '/names2id');
+#ok not -e ($db_flatfile->{index_directory} . '/nodes');
+#ok not -e ($db_flatfile->{index_directory} . '/parents');
+
+## Test removal of temporary index files from test_output_dir folder
+## (since test_output_dir() =~ m/^$Bio::Root::IO::TEMPDIR/)
+#ok $db_flatfile = Bio::DB::Taxonomy->new(
+#    -source    => 'flatfile',
+#    -directory => $temp_dir,
+#    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
+#    -namesfile => test_input_file('taxdump', 'names.dmp'),
+#    -force     => 1,
+#);
+#is $db_flatfile->{index_directory}, $temp_dir, 'removal of temporary index files: test_output_dir()';
+#$db_flatfile->DESTROY;
+#ok not -e ($db_flatfile->{index_directory} . '/id2names');
+#ok not -e ($db_flatfile->{index_directory} . '/names2id');
+#ok not -e ($db_flatfile->{index_directory} . '/nodes');
+#ok not -e ($db_flatfile->{index_directory} . '/parents');
+#
+# Generate the object (and the files) again for the remaining tests
+ok my $db = Bio::DB::Taxonomy->new(
+    -source    => 'flatfile',
+    -directory => $temp_dir,
+    -nodesfile => test_input_file('taxdump', 'nodes.dmp'),
+    -namesfile => test_input_file('taxdump', 'names.dmp'),
+    -force     => 1,
+);
+
+my $id;
+
+is $db->get_num_taxa, 189;
+
+#eval { $id = $db->get_taxonid('Homo sapiens');};
+#skip "Unable to connect to entrez database; no network or server busy?", 38 if $@;
+#
+#is $id, 9606;
+#
+## easy test on human, try out the main Taxon methods
+#ok $n = $db->get_taxon(9606);
+#is $n->id, 9606;
+#is $n->object_id, $n->id;
+#is $n->ncbi_taxid, $n->id;
+#is $n->parent_id, 9605;
+#is $n->rank, 'species';
+#
+#is $n->node_name, 'Homo sapiens';
+#is $n->scientific_name, $n->node_name;
+#is ${$n->name('scientific')}[0], $n->node_name;
+#
+#my %common_names = map { $_ => 1 } $n->common_names;
+#is keys %common_names, 3, ref($db).": common names";
+#ok exists $common_names{human};
+#ok exists $common_names{man};
+#
+#is $n->division, 'Primates';
+#is $n->genetic_code, 1;
+#is $n->mitochondrial_genetic_code, 2;
+## these are entrez-only, data not available in dmp files
+#if ($db eq $db_entrez) {
+#    ok defined $n->pub_date;
+#    ok defined $n->create_date;
+#    ok defined $n->update_date;
+#}
+#
+## briefly test some Bio::Tree::NodeI methods
+#ok my $ancestor = $n->ancestor;
+#is $ancestor->scientific_name, 'Homo';
+## unless set explicitly, Bio::Taxon doesn't return anything for
+## each_Descendent; must ask the database directly
+#ok my @children = $ancestor->db_handle->each_Descendent($ancestor);
+#cmp_ok @children, '>', 0;
+#
+#sleep(3) if $db eq $db_entrez;
+#
+## do some trickier things...
+#ok my $n2 = $db->get_Taxonomy_Node('89593');
+#is $n2->scientific_name, 'Craniata';
+#
+## briefly check we can use some Tree methods
+#my $tree = Bio::Tree::Tree->new();
+#is $tree->get_lca($n, $n2)->scientific_name, 'Craniata';
+#
+## get lineage_nodes
+#my @nodes = $tree->get_nodes;
+#is scalar(@nodes), 0;
+#my @lineage_nodes;
+#@lineage_nodes = $tree->get_lineage_nodes($n->id); # read ID, only works if nodes have been added to tree
+#is scalar @lineage_nodes, 0;
+#@lineage_nodes = $tree->get_lineage_nodes($n);     # node object always works
+#cmp_ok(scalar @lineage_nodes, '>', 20);
+#
+## get lineage string
+#like($tree->get_lineage_string($n), qr/cellular organisms;Eukaryota/);
+#like($tree->get_lineage_string($n,'-'), qr/cellular organisms-Eukaryota/);
+#like($tree->get_lineage_string($n2), qr/cellular organisms;Eukaryota/);
+#
+## can we actually form a Tree and use other Tree methods?
+#ok $tree = Bio::Tree::Tree->new(-node => $n);
+#cmp_ok($tree->number_nodes, '>', 20);
+#cmp_ok(scalar($tree->get_nodes), '>', 20);
+#is $tree->find_node(-rank => 'genus')->scientific_name, 'Homo';
+#
+## check that getting the ancestor still works now we have explitly set the
+## ancestor by making a Tree
+#is $n->ancestor->scientific_name, 'Homo';
+#
+#sleep(3) if $db eq $db_entrez;
+#
+#ok $n = $db->get_Taxonomy_Node('1760');
+#is $n->scientific_name, 'Actinobacteria';
+#
+#sleep(3) if $db eq $db_entrez;
+#
+## entrez isn't as good at searching as flatfile, so we have to special-case
+#my @ids = sort $db->get_taxonids('Chloroflexi');
+#is scalar @ids, 2;
+#is_deeply \@ids, [200795, 32061];
+#
+#$id = $db->get_taxonids('Chloroflexi (class)');
+#$db eq $db_entrez ? is($id, undef) : is($id, 32061);
+#
+#@ids = $db->get_taxonids('Rhodotorula');
+#cmp_ok @ids, '>=' , 8;
+#@ids = $db->get_taxonids('Rhodotorula <Microbotryomycetidae>');
+#is @ids, 1;
+#is $ids[0], 231509;
+
+
+# get_lca should work on nodes from different databases
+#SKIP: {
+#    test_skip(-tests => 9, -requires_networking => 1);
+#
+#    # check that the result is the same as if we are retrieving from the same DB
+#    # flatfile
+#    $h_flat = $db_flatfile->get_taxon(-name => 'Homo');
+#    my $h_flat2 = $db_flatfile->get_taxon(-name => 'Homo sapiens');
+#    ok my $tree_functions = Bio::Tree::Tree->new();
+#    is $tree_functions->get_lca($h_flat, $h_flat2)->scientific_name, 'Homo', 'get_lca() within flatfile db';
+#
+#    # entrez
+#    my $h_entrez;
+#    eval { $h_entrez = $db_entrez->get_taxon(-name => 'Homo sapiens');};
+#    skip "Unable to connect to entrez database; no network or server busy?", 7 if $@;
+#    my $h_entrez2;
+#    eval { $h_entrez2 = $db_entrez->get_taxon(-name => 'Homo');};
+#    skip "Unable to connect to entrez database; no network or server busy?", 7 if $@;
+#    ok $tree_functions = Bio::Tree::Tree->new();
+#    is $tree_functions->get_lca($h_entrez, $h_entrez2)->scientific_name, 'Homo', 'get_lca() within entrez db';
+#
+#    ok $tree_functions = Bio::Tree::Tree->new();
+#    # mixing entrez and flatfile
+#    TODO:{
+#        local $TODO = 'Mixing databases for get_lca() not working, see bug #3416';
+#        is $tree_functions->get_lca($h_flat, $h_entrez)->scientific_name, 'Homo', 'get_lca() mixing flatfile and remote db';
+#    }
+#    # even though the species taxa for Homo sapiens from list and flat databases
+#    # have the same internal id, get_lca won't work because they have different
+#    # roots and descendents
+#    $h_list = $db_list->get_taxon(-name => 'Homo sapiens');
+#    is $h_list->ancestor->internal_id, $h_flat->internal_id;
+#    ok ! $tree_functions->get_lca($h_flat, $h_list);
+#
+#    # but we can form a tree with the flat node then remove all the ranks we're
+#    # not interested in and try again
+#    $tree = Bio::Tree::Tree->new(-node => $h_flat);
+#    $tree->splice(-keep_rank => \@ranks);
+#    is $tree->get_lca($h_flat, $h_list)->scientific_name, 'Homo';
+#}
+
+# Some tests carried over from flatfile and others that would be nice to pass
+
+## ideas from taxonomy2tree.PLS that let us make nice tree, using
+## Bio::Tree::TreeFunctionsI methods; this is a weird and trivial example just
+## because our test flatfile database only has the full lineage of one species
+#undef $tree;
+#for my $name ('Human', 'Hominidae') {
+#  my $ncbi_id = $db_flatfile->get_taxonid($name);
+#  if ($ncbi_id) {
+#    my $node = $db_flatfile->get_taxon(-taxonid => $ncbi_id);
+#
+#    if ($tree) {
+#        ok $tree->merge_lineage($node);
+#    }
+#    else {
+#        ok $tree = Bio::Tree::Tree->new(-node => $node);
+#    }
+#  }
+#}
+#is $tree->get_nodes, 30;
+#$tree->contract_linear_paths;
+#my $ids = join(",", map { $_->id } $tree->get_nodes);
+#is $ids, '131567,9606';
+
+#SKIP: {
+#    test_skip(-tests => 1, -requires_networking => 1);
+#    eval {$db_entrez->get_taxon(10090);};
+#    skip "Unable to connect to entrez database; no network or server busy?", 1 if $@;
+#
+#    my $lca = $db_entrez->get_taxon(314146);
+#    my @descs = $db_entrez->get_all_Descendents($lca);
+#    cmp_ok @descs, '>=', 17;
+#}
+
+
+
+done_testing();
-- 
2.11.4.GIT