Compare revisions

c5ef98fa · be16ca3b · 229bc669 · 6cf66877 · d5819834 · bfaf8090
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,110 +2,79 @@
 # Test-job template
 #

-.ensembl_test_template:
-  image: dockerhub.ebi.ac.uk/ensembl-infrastructure/ensembl-ci-docker-images:${PERL_VERSION}
+variables:
+   USER: "gitlabci"
+   MYSQL_ROOT_PASSWORD: "n0t4t4l1s3cur3!"

+.ensembl_test_template:
  services:
-    - mysql:5.6
+     - name: mysql:5.7
+       alias: mysqldb

-  variables:
-    # FIXME: set some password for both users
-    MYSQL_ALLOW_EMPTY_PASSWORD: "yes"
-    MYSQL_USER: "travis"
-    MYSQL_PASSWORD: ""
-    USER: "gitlabci"
+  image: dockerhub.ebi.ac.uk/ensembl-infrastructure/ensembl-ci-docker-images:${PERL_VERSION}
+  tags:
+    - infra

  before_script:
-    - apt-get update
-    - apt-get install -y build-essential cpanminus git
-    - apt-get install -y default-libmysqlclient-dev default-mysql-client
-    - apt-get install -y libssl-dev sqlite3
-    - git clone --branch=master --depth=1 https://github.com/Ensembl/ensembl-test.git
-    - git clone --branch=master --depth=1 https://github.com/Ensembl/ensembl-io.git
-    - git clone --branch=master --depth=1 https://github.com/Ensembl/ensembl-variation.git
-    - git clone --branch=master --depth=1 https://github.com/Ensembl/ensembl-compara.git
-    - git clone --branch=release-1-6-924 --depth=1 https://github.com/bioperl/bioperl-live.git
-    - cpanm -v --installdeps --notest . --with-all-features
-    - ( cd ensembl-test && cpanm -v --installdeps --notest . )
-#    - ( cd ensembl-io && cpanm -v --installdeps --notest . )
-#    - ( cd ensembl-variation && cpanm -v --installdeps --notest . )
-    - ( cd ensembl-compara && cpanm -v --installdeps --notest . )
-    - cpanm -n Devel::Cover::Report::Coveralls
-    - cpanm -n DBD::SQLite
+    - echo "CI_COMMIT_BRANCH = $CI_COMMIT_BRANCH"
+    - echo "CI_COMMIT_REF_NAME = $CI_COMMIT_REF_NAME"
+    - export ENSEMBL_BRANCH='main'
+    - export ENSEMBL_VER=$(echo $TRAVIS_BRANCH | grep -P -o '(?<=version[\W_]|fix[\W_]|release[\W_])(\d+)')
+    - if [[ $ENSEMBL_VER =~ [0-9]+ ]]; then ENSEMBL_BRANCH="release/$ENSEMBL_VER"; fi
+    - git clone --branch=$ENSEMBL_BRANCH --depth=1 https://github.com/Ensembl/ensembl-test.git
+    - git clone --branch=$ENSEMBL_BRANCH --depth=1 https://github.com/Ensembl/ensembl-io.git
+    - git clone --branch=$ENSEMBL_BRANCH --depth=1 https://github.com/Ensembl/ensembl-variation.git
+    - git clone --branch=$ENSEMBL_BRANCH --depth=1 https://github.com/Ensembl/ensembl-compara.git
+    - cpanm --installdeps --notest . --with-all-features
+    - cpanm -n Devel::Cover::Report::Coveralls DBD::SQLite
    - cp travisci/MultiTestDB.conf.gitlabci.mysql  modules/t/MultiTestDB.conf.mysql
    - cp travisci/MultiTestDB.conf.travisci.SQLite modules/t/MultiTestDB.conf.SQLite
    - cp travisci/testdb.conf.gitlabci.mysql  testdb.conf.mysql
    - cp travisci/testdb.conf.travisci.SQLite testdb.conf.SQLite
-    - mysql -u root -h mysql -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
+
+  tags:
+    - dind

 #
 # Test jobs
 #

-test:perl5.14-sqlite:
-  stage: test
+test:perl5.26-sqlite:
  extends: .ensembl_test_template
  variables:
-    PERL_VERSION: "5.14"
+    PERL_VERSION: "5.26"
    COVERALLS: "false"
    DB: "sqlite"
  script:
    - ./travisci/harness.sh

-test:perl5.30-mysql:
-  stage: test
+test:perl5.26-mysql:
  extends: .ensembl_test_template
  variables:
-    PERL_VERSION: "5.30"
+    PERL_VERSION: "5.26"
    # Note: relies on the secret variable COVERALLS_REPO_TOKEN for report uploads to work
-    COVERALLS: "true"
+    COVERALLS: "false"
    DB: "mysql"
  script:
    - ./travisci/harness.sh

+test:perl5.38-sqlite:
+  stage: test
+  tags:
+    - infra
+  extends: .ensembl_test_template
+  variables:
+    PERL_VERSION: "5.38"
+    COVERALLS: "false"
+    DB: "sqlite"
+  script:
+    - ./travisci/harness.sh
+
 #
 # Triggers for dependent builds
 #

-# The template. It doesn't presently support PRs before they are
-# merged (would need extended run condition and better selection of
-# downstream branches) - but then again, we do not trigger dependent
-# builds for PRs on Travis either.
-.dependent_template:
-  stage: test
-  only:
-    - master
-    - /^release/\d+$/
-
-# Actual trigger jobs
-
-# ensembl-rest; disabled for now because that repo a) hasn't got
-# GitLab-CI config yet, and b) is still on the list in
-# trigger-dependent-build.sh.
-.test:trigger_rest:
-  extends: .dependent_template
-  trigger:
-    project: ensembl-gh-mirror/ensembl-rest
-    # Use the same branch as in this project
-    branch: ${CI_COMMIT_REF_NAME}
-
-# Dependent builds on Travis
-# Relies on the secret variable TRAVIS_AUTH_TOKEN to actually work,
-# moreover the account associated with the token must have write
-# access to *all* dependent repositories; to be exact what it needs
-# is the Travis 'create_request' permission but Travis permissions are
-# generated from GitHub ones and it seems that in order to have
-# 'create_request' on the latter one requires 'write' on the former.
-test:trigger_travis:
-  extends: .dependent_template
-  image: alpine:3.10
-  variables:
-    AUTH_TOKEN: ${TRAVIS_AUTH_TOKEN}
-    TRAVIS_REPO_SLUG: ${CI_PROJECT_PATH}
-    TRAVIS_BRANCH: ${CI_COMMIT_REF_NAME}
-    TRAVIS_COMMIT: ${CI_COMMIT_SHA}
-    # Safe as long as run conditions above do not include merge requests
-    TRAVIS_PULL_REQUEST: "false"
-  script:
-    - apk add --no-cache bash curl python3
-    - ${CI_PROJECT_DIR}/travisci/trigger-dependent-build.sh
+# Removed the dependent builds triggered from GitLab
+# Travis cfg is not allowing concurrent build anymore
+# and dep build requests are timing out
+# Better remove them - for now
--- a/.travis.yml
+++ b/.travis.yml
 language: perl

 dist:
-  - trusty
+  - focal

 services:
  - mysql

 perl:
-  - '5.14'
  - '5.26'
-  - '5.30'
+  - '5.32'

 env:
  matrix:
-  - COVERALLS=true  DB=mysql
+  - COVERALLS=true  DB=mysql COVERALLS_REPO_TOKEN=${{secret.COVERALLS_REPO_TOKEN}}
  - COVERALLS=false DB=mysql
  - COVERALLS=false DB=sqlite
  global:
  - secure: Ju069PzB8QZG3302emIhyCEEQfVfVsiXy0nGcR6hue+vW9nE82NnOEZHbZIwUCXEjUaZRMVQ31Em70Ky22OrLK4D59bs2ClH21u8URDGD/cn7JNPGWFrgxuaXQKMQrw72doeB0+w1+ShURtqM41vITjinyU3y34RZ1NcbDwYSZI=

-addons:
-  apt:
-    packages:
-    - unzip
-
 before_install:
  - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
  - export PATH=$PWD/ensembl-git-tools/bin:$PATH
-  - export ENSEMBL_BRANCH='master'
-  - export SECONDARY_BRANCH='main'
+  - export ENSEMBL_BRANCH='main'
  - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH"
-  - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; export SECONDARY_BRANCH=$TRAVIS_BRANCH; fi
+  - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; fi
  - echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
-  - echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
-  - git-ensembl --clone --depth 1 --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH ensembl-test
-  - git-ensembl --clone --depth 1 --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH ensembl-io
-  - git-ensembl --clone --depth 1 --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH ensembl-variation
-  - git-ensembl --clone --depth 1 --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH ensembl-compara
+  - git-ensembl --clone --depth 1 --branch $ENSEMBL_BRANCH ensembl-test
+  - git-ensembl --clone --depth 1 --branch $ENSEMBL_BRANCH ensembl-io
+  - git-ensembl --clone --depth 1 --branch $ENSEMBL_BRANCH ensembl-variation
+  - git-ensembl --clone --depth 1 --branch $ENSEMBL_BRANCH ensembl-compara
  - git clone -b release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git

 install:
-  - cpanm -v --sudo --installdeps --notest . --with-all-features
-  - cpanm -n --sudo Devel::Cover Devel::Cover::Report::Coveralls Test::Exception Moose Devel::Cycle Test::Warnings 
-  - cpanm -n --sudo DBD::SQLite JSON 
+  - cpanm -v --sudo --notest XML::LibXML # https://github.com/shlomif/perl-XML-LibXML/pull/87
+  - cpanm -v --sudo --installdeps --notest --with-all-features .
  - cp travisci/MultiTestDB.conf.travisci.mysql  modules/t/MultiTestDB.conf.mysql
  - cp travisci/MultiTestDB.conf.travisci.SQLite modules/t/MultiTestDB.conf.SQLite
  - cp travisci/testdb.conf.travisci.mysql  testdb.conf.mysql
@@ -50,35 +41,16 @@ install:
  - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
  - mysql -u root -h localhost -e 'SET GLOBAL local_infile=1'

-before_script:
-  - rm -f "$HOME/.ensemblapi_no_version_check"
-
-script: 
+script:
  - "./travisci/harness.sh"

 jobs:
-  include:
-    - dist: focal
-      perl: '5.30' 
-      env: COVERALLS=false  DB=mysql
  exclude:
-    - perl: '5.14'
-      env: COVERALLS=false DB=mysql
-    - perl: '5.14'
-      env: COVERALLS=true  DB=mysql
+    - perl: '5.32'
+      env: COVERALLS=true DB=mysql COVERALLS_REPO_TOKEN=${{secret.COVERALLS_REPO_TOKEN}}
    - perl: '5.26'
-      env: COVERALLS=false DB=sqlite
-    - perl: '5.26'
-      env: COVERALLS=false DB=mysql
-    - perl: '5.30'
-      env: COVERALLS=false DB=sqlite
-      dist: trusty
-    - perl: '5.30'
      env: COVERALLS=false DB=mysql
-      dist: trusty
-    - perl: '5.30'
-      env: COVERALLS=true DB=mysql
-      dist: trusty
+

 notifications:
  email:

--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -9,11 +9,11 @@ We also invite you to read our code of conduct (http://www.ensembl.org/info/abou

 1. Fork the ensembl repository
 2. Switch to the branch you want to edit
-  * Consider using feature branches over editing master
+  * Consider using feature branches over editing main
 3. Hack away and commit with a useful commit message
  * First line is short but descriptive
  * Other lines are more explanatory
-4. Make sure your forked master is up-to date with origin and rebase if needed
+4. Make sure your forked main is up-to date with origin and rebase if needed
 6. Push
 7. Create a pull request
 8. Communicate what the change is
@@ -69,19 +69,19 @@ git remote add upstream https://github.com/Ensembl/ensembl.git

 ## Switching Branch

-By default Ensembl projects have a default branch of the **latest stable release**. If you are contributing a fix for a specific release then please remain there; otherwise switch to master.
+By default Ensembl projects have a default branch of the **latest stable release**. If you are contributing a fix for a specific release then please remain there; otherwise switch to main.

 ```
-git checkout --track -b master origin/master
+git checkout --track -b main origin/main
 ```

-To help improve your hacking time consider developing on a branch from master. This will allow you to bring in changes from upstream and integrate them into your fork without fear of merge conflicts. The following prefixes are available to use:
+To help improve your hacking time consider developing on a branch from main. This will allow you to bring in changes from upstream and integrate them into your fork without fear of merge conflicts. The following prefixes are available to use:

 * _feature/_ - A new feature going into a repository
 * _hotfix/_ - Fixes to be integrated into a branch
 * _experimental/_ - Experimental feature with no guarentee about hash stability

-Switch to a new branch once you are on master:
+Switch to a new branch once you are on main:

 ```
 git checkout -b hotfix/quickfixtoadaptor
@@ -106,19 +106,19 @@ retrieval system but rather the MySQL last insert id variable.

 Try also to minimise branches within your code base. If we see too many we will ask you to rebase/squish.

-## Syncing master with upstream, rebasing your changes and pushing
+## Syncing main with upstream, rebasing your changes and pushing

-First switch to master and pull in new changes from upstream held on master. This will bring those changes down and attempt to merge your local master with _upstream/master_. If you have changes on master be aware that this will probably require a merge commit. Staying away from master is a good idea.
+First switch to main and pull in new changes from upstream held on main. This will bring those changes down and attempt to merge your local main with _upstream/main_. If you have changes on main be aware that this will probably require a merge commit. Staying away from main is a good idea.

 ```
-git checkout master
-git pull upstream master
+git checkout main
+git pull upstream main
 ```
-Once the changes are down rebase your branch against master:
+Once the changes are down rebase your branch against main:

 ```
 git checkout hotfix/quickfixtoadaptor
-git rebase master
+git rebase main
 ```
 Now push to origin:

@@ -132,7 +132,7 @@ https://help.github.com/articles/using-pull-requests

 Go to your GitHub fork's page, switch to your branch and click on the _Compare and Review_ button. This will start the merge. Then click on the top left +- file icon and edit accordingly:

-* Switch the base branch to _master_
+* Switch the base branch to _main_

 This ensures you are submitting your change against the right branch in Ensembl. For more information see [GitHub's documentation on doing this](https://help.github.com/articles/using-pull-requests#changing-the-branch-range-and-destination-repository).


--- a/LICENSE
+++ b/LICENSE
-                                Apache License
+
+                                 Apache License
                           Version 2.0, January 2004
                        http://www.apache.org/licenses/

@@ -178,7 +179,7 @@
   APPENDIX: How to apply the Apache License to your work.

      To apply the Apache License to your work, attach the following
-      boilerplate notice, with the fields enclosed by brackets "{}"
+      boilerplate notice, with the fields enclosed by brackets "[]"
      replaced with your own identifying information. (Don't include
      the brackets!)  The text should be enclosed in the appropriate
      comment syntax for the file format. We also recommend that a
@@ -186,8 +187,7 @@
      same "printed page" as the copyright notice for easier
      identification within third-party archives.

-   Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-   Copyright [2016-2022] EMBL-European Bioinformatics Institute
+   Copyright [yyyy] [name of copyright owner]

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
@@ -201,41 +201,3 @@
   See the License for the specific language governing permissions and
   limitations under the License.

-
-ENSEMBL CORE PROJECT SUBCOMPONENTS
-
-The Ensembl Core Project includes a number of subcomponents with
-separate copyright notices and license terms. Your use of the source
-code for the these subcomponents is subject to the terms and
-conditions of the following licenses.
-
-COMPONENT: modules/Bio/EnsEMBL/Utils/Cache.pm
-
-Code has been renamed from Tie::Cache to 
-Bio::EnsEMBL::Utils::Cache and originally distributed on CPAN.
-
-Copyright (c) 1999-2002 Joshua Chamas, Chamas Enterprises Inc.  
-Sponsored by development on NodeWorks http://www.nodeworks.com
-
-All rights reserved. This program is free software; 
-you can redistribute it and/or modify it under the same 
-terms as Perl itself.
-
-COMPONENT: misc-scripts/doxygen_filter/EnsEMBL/Filter.pm and 
-           misc-scripts/doxygen_filter/EnsEMBL/PerlFilter.pm. 
-
-Both portions of code were based on the following agreement; 
-PerlFilter.pm has seen significant re-writing but derives from the 
-original source.
-
-Doxygen Pre-Processor for Perl
-Copyright (C) 2002  Bart Schuller
-Copyright (C) 2006  Phinex Informatik AG
-All Rights Reserved
-
-Doxygen Filter is free software; you can redistribute it and/or modify
-it under the same terms as Perl itself.
-
-Larry Wall's 'Artistic License' for perl can be found in
-http://www.perl.com/pub/a/language/misc/Artistic.html
-
--- a/NOTICE
+++ b/NOTICE
+Ensembl
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
+
+This product includes software developed at:
+- EMBL-European Bioinformatics Institute
+- Wellcome Trust Sanger Institute
+
+ENSEMBL CORE PROJECT SUBCOMPONENTS
+
+The Ensembl Core Project includes a number of subcomponents with
+separate copyright notices and license terms. Your use of the source
+code for the these subcomponents is subject to the terms and
+conditions of the following licenses.
+
+COMPONENT: modules/Bio/EnsEMBL/Utils/Cache.pm
+
+Code has been renamed from Tie::Cache to 
+Bio::EnsEMBL::Utils::Cache and originally distributed on CPAN.
+
+Copyright (c) 1999-2002 Joshua Chamas, Chamas Enterprises Inc.  
+Sponsored by development on NodeWorks http://www.nodeworks.com
+
+All rights reserved. This program is free software; 
+you can redistribute it and/or modify it under the same 
+terms as Perl itself.
+
+COMPONENT: misc-scripts/doxygen_filter/EnsEMBL/Filter.pm and 
+           misc-scripts/doxygen_filter/EnsEMBL/PerlFilter.pm. 
+
+Both portions of code were based on the following agreement; 
+PerlFilter.pm has seen significant re-writing but derives from the 
+original source.
+
+Doxygen Pre-Processor for Perl
+Copyright (C) 2002  Bart Schuller
+Copyright (C) 2006  Phinex Informatik AG
+All Rights Reserved
+
+Doxygen Filter is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
--- a/README.md
+++ b/README.md
 # Ensembl Core API

-[![Build Status](https://travis-ci.org/Ensembl/ensembl.svg?branch=master)][travis]
-[![Coverage Status](https://coveralls.io/repos/github/Ensembl/ensembl/badge.svg?branch=master)][coveralls]
+[![Build Status](https://travis-ci.org/Ensembl/ensembl.svg?branch=main)][travis]
+[![Coverage Status](https://coveralls.io/repos/github/Ensembl/ensembl/badge.svg?branch=main)][coveralls]

 [travis]: https://travis-ci.org/Ensembl/ensembl
 [coveralls]: https://coveralls.io/github/Ensembl/ensembl
@@ -17,7 +17,7 @@ To clone the Ensembl Core API, use the following command:
 ```
 git clone https://github.com/Ensembl/ensembl.git
 ```
-Alternatively, you can download the files in gzipped TAR format from our [FTP site](ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz).
+Alternatively, you can download the files in gzipped TAR format from our [FTP site](https://ftp.ensembl.org/pub/ensembl-api.tar.gz).

 ## API requirements
 In order to use the Ensembl Core API, an installation of [BioPerl 1.6.924 core modules](https://github.com/bioperl/bioperl-live/archive/release-1-6-924.zip) (bioperl-live) is required.

--- a/cpanfile
+++ b/cpanfile
 requires 'DBI';
-requires 'DBD::mysql';
+requires 'DBD::mysql', '< 5.0'; # newer versions do not support MySQL 5
+requires 'DBD::SQLite';
 requires 'HTTP::Tiny';
 requires 'IO::Compress::Gzip';
 requires 'URI::Escape';
 requires 'Config::IniFiles';
+requires 'Gzip::Faster';
+requires 'List::MoreUtils';
+requires 'JSON';

 test_requires 'Test::Warnings';
 test_requires 'Test::Differences';
@@ -13,6 +17,8 @@ test_requires 'Test::Deep';
 test_requires 'Test::More';
 test_requires 'Devel::Peek';
 test_requires 'Devel::Cycle';
+test_requires 'Devel::Cover';
+test_requires 'Devel::Cover::Report::Coveralls';
 test_requires 'Error';
 test_requires 'PadWalker';
 test_requires 'Test::Builder::Module';
@@ -38,6 +44,7 @@ feature 'xref_mapping', 'Xref mapping pipeline' => sub {
  requires 'Text::Glob';
  requires 'URI';
  requires 'XML::LibXML';
+  requires 'Text::Unidecode';

  test_requires 'Config::General';
  test_requires 'Perl::Critic::Moose';

--- a/misc-scripts/CreateFile4CopyDBoverServer.pl
+++ b/misc-scripts/CreateFile4CopyDBoverServer.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/alt_alleles/alt_alleles.pl
+++ b/misc-scripts/alt_alleles/alt_alleles.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/annual_copyright_updater.sh
+++ b/misc-scripts/annual_copyright_updater.sh
 #!/bin/bash
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -37,15 +37,32 @@ for var in $dirs; do
  search="^\(.*\)\\[\([0-9]*\)\(-*[0-9]*\)\\] EMBL-European Bioinformatics Institute"
  replacement="\1[\2-$year] EMBL-European Bioinformatics Institute"

+  likely_copyright_line=".*[0-9].* EMBL-European Bioinformatics Institute"
+  exception_line="Copyright \\[1999-2015\\] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute"
+
  echo "About to scan $(pwd) for files to replace '$search' with '$replacement'"

-  for file in $(grep -r --files-with-matches "$search" --exclude-dir=.git .); do
-    echo "Replacing date in $file"
+  for file in $(grep -r --files-with-matches "$likely_copyright_line" --exclude-dir=.git .); do
+
+    if [[ $(grep "$search" $file) ]]; then
+      echo "Replacing date in $file"
+    fi
+
    if [ "$(uname)" = "Darwin" ]; then
      LC_CTYPE=C LANG=C sed -i '' -e "s/$search/$replacement/g" $file
    else
      sed --in-place -e "s/$search/$replacement/g" $file
    fi
+
+    # If the line matches the more general $likely_copyright_line, but not the more specific $search regex that we
+    # know how to update, and isn't the $exception_line, then we warn the user that the line is likely a copyright
+    # line that we don't know how to update.
+    grep "$likely_copyright_line" $file | while read -r line ; do
+      if [[ $(echo $line | grep -v "$search") && $(echo $line | grep -v "$exception_line") ]]; then
+        echo "Unable to replace date in $file.  The line is: $line"
+      fi
+    done
+
  done

  cd $original_wd

--- a/misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm
+++ b/misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm
 =head1 LICENSE

-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2022] EMBL-European Bioinformatics Institute
+See the NOTICE file distributed with this work for additional information
+regarding copyright ownership.

 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/EXAMPLE.use_mapping.pl
+++ b/misc-scripts/assembly/EXAMPLE.use_mapping.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/align_by_clone_identity.pl
+++ b/misc-scripts/assembly/align_by_clone_identity.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/align_nonident_regions.pl
+++ b/misc-scripts/assembly/align_nonident_regions.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/align_nonident_regions_wrapper.pl
+++ b/misc-scripts/assembly/align_nonident_regions_wrapper.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/check_mapping.pl
+++ b/misc-scripts/assembly/check_mapping.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/cleanup_tmp_tables.sql
+++ b/misc-scripts/assembly/cleanup_tmp_tables.sql
-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-- Copyright [2016-2022] EMBL-European Bioinformatics Institute
+-- See the NOTICE file distributed with this work for additional information
+-- regarding copyright ownership.
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/compare_assemblies.pl
+++ b/misc-scripts/assembly/compare_assemblies.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/conservation_statistics.pl
+++ b/misc-scripts/assembly/conservation_statistics.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

--- a/misc-scripts/assembly/ensembl_assembly_to_chain.pl
+++ b/misc-scripts/assembly/ensembl_assembly_to_chain.pl
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2022] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
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