New script to automatically create fenced SQL patches

scripts/create_sql_patches.pl

+#!/usr/bin/env perl
+# Copyright [1999-2015] 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.
+
+use strict;
+use warnings;
+
+    # Finding out own path in order to reference own components (including own modules):
+use Cwd            ();
+use File::Basename ();
+BEGIN {
+    $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) );
+    unshift @INC, $ENV{'EHIVE_ROOT_DIR'}.'/modules';
+}
+
+use DateTime;
+use File::Basename;
+use File::Copy;
+use Getopt::Long;
+
+use Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
+
+my $opts = {
+    driver => [],
+    date    => undef, # this means today
+    help => 0,
+};
+my @args = ('driver=s@', 'date=s', 'help|h');
+
+my $parse = GetOptions($opts, @args);
+if(!$parse) {
+  print STDERR "Could not parse the given arguments. Please consult the help\n";
+  usage();
+  exit 1;
+}
+
+# Print usage on '-h' command line option
+if ($opts->{help}) {
+  usage();
+  exit;
+}
+
+$opts->{driver} = [qw(mysql sqlite pgsql)] unless scalar(@{$opts->{driver}});
+$opts->{date} = DateTime->now->ymd('-') unless $opts->{date};
+
+my $code_sql_schema_version = Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_code_sql_schema_version()
+    || die "Could not establish code_sql_schema_version, please check that 'EHIVE_ROOT_DIR' environment variable is set correctly\n";
+
+foreach my $driver (@{$opts->{driver}}) {
+    -s "$ENV{'EHIVE_ROOT_DIR'}/sql/patch_$opts->{date}.$driver" && die "$ENV{'EHIVE_ROOT_DIR'}/sql/patch_$opts->{date}.$driver already exists ! Remove this file or change the patch date\n";
+    system("sed 's/___EXPECTED_SCHEMA_VERSION___/$code_sql_schema_version/' '$ENV{'EHIVE_ROOT_DIR'}/sql/template_patch.$driver' > '$ENV{'EHIVE_ROOT_DIR'}/sql/patch_$opts->{date}.$driver'");
+    -s "$ENV{'EHIVE_ROOT_DIR'}/sql/patch_$opts->{date}.$driver" || die "Could not copy $ENV{'EHIVE_ROOT_DIR'}/sql/template_patch.$driver to $ENV{'EHIVE_ROOT_DIR'}/sql/patch_$opts->{date}.$driver\n";
+}
+
+sub usage {
+    print <<EOT;
+Usage:
+\t$0 [-date <day_of_the_patch>] [-driver <name_of_first_driver>] [-driver <name_of_second_driver>] ...
+\t$0 -h
+
+\t-date\n\t\tdate in ISO format, e.g. 2015-02-14. Defaults to the current date
+\t-driver (can be repeated)\n\t\tdriver for which create a patch. Defaults to MySQL, SQLite, and Postgre
+\t-h|--help\n\t\tdisplay this help text
+
+EOT
+}
+

sql/template_patch.mysql

+
+-- ---------------------------------------------------------------------------------------------------
+
+SET @expected_version = ___EXPECTED_SCHEMA_VERSION___;
+
+    -- make MySQL stop immediately after it encounters division by zero:
+SET SESSION sql_mode='TRADITIONAL';
+
+    -- warn that we detected the schema version mismatch:
+SELECT CONCAT(  'The patch only applies to schema version ',
+                @expected_version,
+                ', but the current schema version is ',
+                meta_value,
+                ', so skipping the rest.') AS ''
+    FROM hive_meta WHERE meta_key='hive_sql_schema_version' AND meta_value<>@expected_version;
+
+    -- cause division by zero only if current version differs from the expected one:
+INSERT INTO hive_meta (meta_key, meta_value)
+    SELECT 'this_should_never_be_inserted', 1 FROM hive_meta WHERE NOT 1/(meta_key<>'hive_sql_schema_version' OR meta_value=@expected_version);
+
+SELECT CONCAT(  'The patch seems to be compatible with schema version ',
+                @expected_version,
+                ', applying the patch...') AS '';
+
+    -- Now undo the change so that we could patch potentially non-TRADITIONAL schema:
+SET SESSION sql_mode='';
+
+-- ----------------------------------<actual_patch> -------------------------------------------------
+
+
+
+
+-- ----------------------------------</actual_patch> -------------------------------------------------
+
+
+    -- increase the schema version by one:
+UPDATE hive_meta SET meta_value=meta_value+1 WHERE meta_key='hive_sql_schema_version';

sql/template_patch.pgsql

+
+-- ---------------------------------------------------------------------------------------------------
+
+\set expected_version ___EXPECTED_SCHEMA_VERSION___
+
+\set ON_ERROR_STOP on
+
+    -- warn that we detected the schema version mismatch:
+SELECT ('The patch only applies to schema version '
+    || CAST(:expected_version AS VARCHAR)
+    || ', but the current schema version is '
+    || meta_value
+    || ', so skipping the rest.') as incompatible_msg
+    FROM hive_meta WHERE meta_key='hive_sql_schema_version' AND meta_value!=CAST(:expected_version AS VARCHAR);
+
+    -- cause division by zero only if current version differs from the expected one:
+INSERT INTO hive_meta (meta_key, meta_value)
+   SELECT 'this_should_never_be_inserted', 1 FROM hive_meta WHERE 1 != 1/CAST( (meta_key!='hive_sql_schema_version' OR meta_value=CAST(:expected_version AS VARCHAR)) AS INTEGER );
+
+SELECT ('The patch seems to be compatible with schema version '
+    || CAST(:expected_version AS VARCHAR)
+    || ', applying the patch...') AS compatible_msg;
+
+
+-- ----------------------------------<actual_patch> -------------------------------------------------
+
+
+
+-- ----------------------------------</actual_patch> -------------------------------------------------
+
+
+    -- increase the schema version by one:
+UPDATE hive_meta SET meta_value= (CAST(meta_value AS INTEGER) + 1) WHERE meta_key='hive_sql_schema_version';

sql/template_patch.sqlite

+
+-- ---------------------------------------------------------------------------------------------------
+
+CREATE TEMPORARY VIEW exp_ver AS SELECT "___EXPECTED_SCHEMA_VERSION___" AS expected_version;
+
+.bail ON
+
+SELECT ('The patch only applies to schema version '
+    || expected_version
+    || ', but the current schema version is '
+    || meta_value
+    || ', skipping the rest.') AS ''
+    FROM hive_meta JOIN exp_ver WHERE meta_key='hive_sql_schema_version' AND meta_value<>expected_version;
+
+INSERT INTO hive_meta (meta_key, meta_value)
+    SELECT hm.* FROM hive_meta AS hm JOIN exp_ver WHERE meta_key='hive_sql_schema_version' AND meta_value<>expected_version;
+
+SELECT ('The patch seems to be compatible with schema version '
+    || expected_version
+    || ', applying the patch...') AS '' FROM exp_ver;
+
+
+-- ----------------------------------<actual_patch> -------------------------------------------------
+
+
+
+-- ----------------------------------</actual_patch> -------------------------------------------------
+
+
+    -- increase the schema version by one:
+UPDATE hive_meta SET meta_value=meta_value+1 WHERE meta_key='hive_sql_schema_version';