.gitlab-ci.yml

@@ -13,17 +13,17 @@
     MYSQL_ALLOW_EMPTY_PASSWORD: "yes"
     MYSQL_USER: "travis"
     MYSQL_PASSWORD: ""
-    USER: "gitlabci"
+    USER: gitlabci
 
   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=main --depth=1 https://github.com/Ensembl/ensembl-test.git
+    - git clone --branch=main --depth=1 https://github.com/Ensembl/ensembl-io.git
+    - git clone --branch=main --depth=1 https://github.com/Ensembl/ensembl-variation.git
+    - git clone --branch=main --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 . )
@@ -42,15 +42,15 @@
 # Test jobs
 #
 
-test:perl5.14-sqlite:
-  stage: test
-  extends: .ensembl_test_template
-  variables:
-    PERL_VERSION: "5.14"
-    COVERALLS: "false"
-    DB: "sqlite"
-  script:
-    - ./travisci/harness.sh
+# test:perl5.14-sqlite:
+#   stage: test
+#   extends: .ensembl_test_template
+#   variables:
+#     PERL_VERSION: "5.14"
+#     COVERALLS: "false"
+#     DB: "sqlite"
+#   script:
+#     - ./travisci/harness.sh
 
 test:perl5.30-mysql:
   stage: test
@@ -82,12 +82,12 @@ test:perl5.30-mysql:
 # 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}
+# .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,
@@ -96,16 +96,16 @@ test:perl5.30-mysql:
 # 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
+# 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

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=release/107)][travis]
+[![Coverage Status](https://coveralls.io/repos/github/Ensembl/ensembl/badge.svg?branch=release/107)][coveralls]
 
 [travis]: https://travis-ci.org/Ensembl/ensembl
 [coveralls]: https://coveralls.io/github/Ensembl/ensembl

misc-scripts/xref_mapping/XrefParser/RefSeqDatabaseParser.pm

 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2021] EMBL-European Bioinformatics Institute
+Copyright [2016-2022] 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.
@@ -19,7 +19,7 @@ limitations under the License.
 
 # Parse RefSeq data from central database to create species specific xrefs.
 
-package XrefParser::RefSeqGPFFParser;
+package XrefParser::RefSeqDatabaseParser;
 
 use strict;
 use warnings;

misc-scripts/xref_mapping/XrefParser/UniProtDatabaseParser.pm

 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2021] EMBL-European Bioinformatics Institute
+Copyright [2016-2022] 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.
@@ -26,7 +26,7 @@ limitations under the License.
 
 
 
-package XrefParser::UniProtParser;
+package XrefParser::UniProtDatabaseParser;
 
 use strict;
 use warnings;

misc-scripts/xref_mapping/xref_config.ini

@@ -520,6 +520,7 @@ order           = 15
 priority        = 2
 prio_descr      = refseq
 parser          = RefSeqDatabaseParser
+old_parser      = RefSeqGPFFParser
 
 [source RefSeq_dna::gencode]
 # Used by human and mouse
@@ -543,6 +544,7 @@ order           = 15
 priority        = 2
 prio_descr      = refseq
 parser          = RefSeqDatabaseParser
+old_parser      = RefSeqGPFFParser
 
 [source RefSeq_dna::MULTI-complete]
 # Used by phaeodactylum_tricornutum
@@ -822,6 +824,7 @@ order           = 20
 priority        = 3
 prio_descr      = sequence_mapped
 parser          = UniProtDatabaseParser
+old_parser      = UniProtParser
 dependent_on    = MIM
 
 [source Uniprot/SPTREMBL::gencode]
@@ -850,6 +853,7 @@ order           = 20
 priority        = 3
 prio_descr      = sequence_mapped
 parser          = UniProtDatabaseParser
+old_parser      = UniProtParser
 dependent_on    = MIM
 
 [source Uniprot/SWISSPROT::gencode]
@@ -1473,6 +1477,7 @@ source          = EntrezGene::MULTI
 source          = Reactome::MULTI
 source          = RNACentral::MULTI
 source          = RefSeq_dna::MULTI-vertebrate
+source          = RefSeq_peptide::MULTI-vertebrate
 source          = RefSeq_import::otherfeatures
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI

misc-scripts/xref_mapping/xref_config2sql.pl

@@ -187,9 +187,10 @@ foreach my $species_section ( sort( $config->GroupMembers('species') ) )
     print(   "INSERT INTO source_url "
            . "(source_id, species_id, parser)\n" );
 
+    my $parser = (defined($config->val($source_section, 'old_parser')) ? $config->val($source_section, 'old_parser') : $config->val($source_section, 'parser'));
     printf( "VALUES (%d, %d, '%s') ;\n",
             $source_ids{$source_section}, $species_id,
-            $config->val( $source_section, 'parser' ) );
+            $parser );
 
     print("\n");