ENSCORESW-866: allow NULL as default value for karyotype and stain

updated to release 76

modules/Bio/EnsEMBL/ApiVersion.pm

@@ -55,7 +55,7 @@ use base qw( Exporter );
 
 our @EXPORT = qw( software_version );
 
-my $API_VERSION = 75;
+my $API_VERSION = 76;
 
 sub software_version { return $API_VERSION }
 

sql/patch_75_76_a.sql

+-- Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- 
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+-- 
+--      http://www.apache.org/licenses/LICENSE-2.0
+-- 
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+# patch_75_76_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+#   Update schema_version in meta table to 76.
+
+UPDATE meta SET meta_value='76' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_75_76_a.sql|schema_version');

sql/patch_75_76_b.sql

+-- Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- 
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+-- 
+--      http://www.apache.org/licenses/LICENSE-2.0
+-- 
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+# patch_75_76_b.sql
+#
+# Title: NULL default in karyotype
+#
+# Description: Band and stain columns in karyotype can be NULL
+
+ALTER TABLE karyotype MODIFY band VARCHAR(40) DEFAULT NULL;
+ALTER TABLE karyotype MODIFY stain VARCHAR(40) DEFAULT NULL;
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_75_76_b.sql|allow_null_karyotype');
+
+

sql/table.sql

@@ -254,8 +254,8 @@ CREATE TABLE karyotype (
   seq_region_id               INT(10) UNSIGNED NOT NULL,
   seq_region_start            INT(10) UNSIGNED NOT NULL,
   seq_region_end              INT(10) UNSIGNED NOT NULL,
-  band                        VARCHAR(40) NOT NULL,
-  stain                       VARCHAR(40) NOT NULL,
+  band                        VARCHAR(40) DEFAULT NULL,
+  stain                       VARCHAR(40) DEFAULT NULL,
 
   PRIMARY KEY (karyotype_id),
   KEY region_band_idx (seq_region_id,band)
@@ -302,23 +302,15 @@ CREATE TABLE IF NOT EXISTS meta (
 # Add schema type and schema version to the meta table.
 INSERT INTO meta (species_id, meta_key, meta_value) VALUES
   (NULL, 'schema_type',     'core'),
-  (NULL, 'schema_version',  '75');
+  (NULL, 'schema_version',  '76');
 
 # Patches included in this schema file:
 # NOTE: At start of release cycle, remove patch entries from last release.
 # NOTE: Avoid line-breaks in values.
 INSERT INTO meta (species_id, meta_key, meta_value)
-  VALUES (NULL, 'patch', 'patch_74_75_a.sql|schema_version');
+  VALUES (NULL, 'patch', 'patch_75_76_a.sql|schema_version');
 INSERT INTO meta (species_id, meta_key, meta_value)
-  VALUES (NULL, 'patch', 'patch_74_75_b.sql|transcript_source');
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_74_75_c.sql|add_genome_statistics');
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_74_75_d.sql|default_transcript_source');
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_74_75_e.sql|unique_attrib_key');
-INSERT INTO meta (species_id, meta_key, meta_value)
- VALUES (NULL, 'patch', 'patch_74_75_f.sql|longer_code');
+  VALUES (NULL, 'patch', 'patch_75_76_b.sql|allow_null_karyotype');
 
 /**
 @table meta_coord