Merge f63e393 into d835b91

README.md

@@ -3,3 +3,14 @@
 # ensembl-datacheck
 Code for checking Ensembl data
 * [Framework details](framework.md)
+
+## Using git hooks to synchronise the datacheck index
+It's easy to get out of sync between datachecks and the index. There's a
+test for this, so it would eventually get detected, but we can proactively
+avoid the problem with a git hook that automatically updates the index.
+
+To configure this, in your local repository do:
+`ln -s ../../hooks/pre-commit.sh .git/hooks/pre-commit`
+
+Then, whenever you commit, the index will be checked, and updated if
+necessary. To skip the checking, use the `--no-verify` flag.

hooks/pre-commit.sh

@@ -0,0 +1,30 @@
+#!/bin/sh
+#
+# Most commits in this repository will be adding or updating datachecks.
+# It is important to keep the index in-sync with the datacheck metadata;
+# this is simple to do, but easy to forget, so an ideal candidate for
+# automation...
+
+EXIT_STATUS=0
+
+# Stash any changes that aren't part of this commit, otherwise
+# the index would be synced with things we're not committing! 
+git stash -q --keep-index
+
+echo "CHECKING INDEX..."
+if !(perl t/index.t)
+then
+  echo "UPDATING INDEX..."
+  if (perl scripts/create_index.pl)
+  then
+    git add lib/Bio/EnsEMBL/DataCheck/index.json
+  else
+    echo "COMMIT REJECTED: failed to update index."
+    echo "Force the commit with the --no-verify flag (not recommended)."
+    EXIT_STATUS=1
+  fi
+fi
+
+git stash pop -q
+
+exit $EXIT_STATUS

t/Manager.t

@@ -62,17 +62,6 @@ subtest 'Default attributes', sub {
   is_deeply($manager->datacheck_types, [], 'Default datacheck_types correct (empty list)');
 };
 
-subtest 'Datacheck index', sub {
-  my $manager = $module->new();
-  my $index_1 = $manager->read_index();
-
-  my $tmp_index_file = Path::Tiny->tempfile();
-  $manager = $module->new(index_file => "$tmp_index_file");
-  my $index_2 = $manager->write_index();
-
-  is_deeply($index_1, $index_2, 'Index file is up-to-date');
-};
-
 subtest 'TestChecks directory', sub {
   my $manager = $module->new(
     datacheck_dir => $datacheck_dir,

t/index.t

@@ -0,0 +1,34 @@
+# Copyright [2018] 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;
+use feature 'say';
+
+use Bio::EnsEMBL::DataCheck::Manager;
+
+use Path::Tiny;
+use Test::More;
+
+my $module = 'Bio::EnsEMBL::DataCheck::Manager';
+
+my $manager = $module->new();
+my $index_1 = $manager->read_index();
+my $tmp_index_file = Path::Tiny->tempfile();
+$manager = $module->new(index_file => "$tmp_index_file");
+my $index_2 = $manager->write_index();
+
+is_deeply($index_1, $index_2, 'Index file is up-to-date');
+
+done_testing();