Merge pull request #370 from Ensembl/feature/test_db_update

Update test dbs to release 105. Remove duplicate 'drosophila' directory.
Ensembl · May 12, 2021 · 4811a34 · 4811a34
2 parents 4438a5c + b89566b
commit 4811a34
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Showing 82 changed files with 15 additions and 75,292 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/MetaKeyConditional.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/MetaKeyConditional.pm
@@ -183,7 +183,7 @@ sub repeat_analysis {
     else {
       @rep_list = qw("repeatmask_repeatmodeler" "repeatdetector");
     }
-    my $to_skip = join("', '", @rep_list);
+    my $to_skip = join(", ", @rep_list);
 
     my $sql = qq/
       SELECT logic_name FROM
@@ -193,7 +193,7 @@ sub repeat_analysis {
         analysis USING (analysis_id)
       WHERE
         species_id = $species_id
-        AND logic_name NOT IN ('$to_skip')
+        AND logic_name NOT IN ($to_skip)
       GROUP BY
         logic_name
       ORDER BY logic_name

diff --git a/t/test-genome-DBs/collection/core/meta.txt b/t/test-genome-DBs/collection/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	104
+2	\N	schema_version	105
 3	\N	patch	patch_88_89_a.sql|schema_version
 4	1	schema.load_started	2017-05-08 19:14:41
 5	1	schema.load_started	2017-05-08 19:14:45
@@ -189,3 +189,4 @@
 561	\N	patch	patch_101_102_a.sql|schema_version
 562	\N	patch	patch_102_103_a.sql|schema_version
 563	\N	patch	patch_103_104_a.sql|schema_version
+564	\N	patch	patch_104_105_a.sql|schema_version
diff --git a/t/test-genome-DBs/drosophila/core/alt_allele.txt b/t/test-genome-DBs/drosophila/core/alt_allele.txt
diff --git a/t/test-genome-DBs/drosophila/core/alt_allele_attrib.txt b/t/test-genome-DBs/drosophila/core/alt_allele_attrib.txt
diff --git a/t/test-genome-DBs/drosophila/core/alt_allele_group.txt b/t/test-genome-DBs/drosophila/core/alt_allele_group.txt
diff --git a/t/test-genome-DBs/drosophila/core/analysis.txt b/t/test-genome-DBs/drosophila/core/analysis.txt
diff --git a/t/test-genome-DBs/drosophila/core/analysis_description.txt b/t/test-genome-DBs/drosophila/core/analysis_description.txt
diff --git a/t/test-genome-DBs/drosophila/core/assembly.txt b/t/test-genome-DBs/drosophila/core/assembly.txt
diff --git a/t/test-genome-DBs/drosophila/core/assembly_exception.txt b/t/test-genome-DBs/drosophila/core/assembly_exception.txt
diff --git a/t/test-genome-DBs/drosophila/core/associated_group.txt b/t/test-genome-DBs/drosophila/core/associated_group.txt
diff --git a/t/test-genome-DBs/drosophila/core/associated_xref.txt b/t/test-genome-DBs/drosophila/core/associated_xref.txt