ensembl-io merge requestshttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests2020-08-18T09:27:46Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/112ENSCORESW-3526 metakey changed from provider.* to assembly.provider_*2020-08-18T09:27:46ZMarek SzubaENSCORESW-3526 metakey changed from provider.* to assembly.provider_**Created by: ameya1981*
Metakey provider.name/url changed to assembly.provider_name/url.
as per https://www.ebi.ac.uk/panda/jira/browse/ENSINT-361*Created by: ameya1981*
Metakey provider.name/url changed to assembly.provider_name/url.
as per https://www.ebi.ac.uk/panda/jira/browse/ENSINT-361https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/106103 test db patch2020-07-16T15:14:47ZMarek Szuba103 test db patch*Created by: ameya1981*
103 test db patch as part of release SOP*Created by: ameya1981*
103 test db patch as part of release SOPhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/105Bugfix/filechameleon gtf error2020-09-02T10:34:56ZMarek SzubaBugfix/filechameleon gtf error*Created by: s-mm*
Fix for [ENSCORESW-3150](https://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-3150). Code modified to handle multidimensional hash. This fix should be combined with changes in
`format-transcriber/lib/Bio/FormatTranscri...*Created by: s-mm*
Fix for [ENSCORESW-3150](https://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-3150). Code modified to handle multidimensional hash. This fix should be combined with changes in
`format-transcriber/lib/Bio/FormatTranscriber.pm`. https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/102add try::tiny2020-07-08T11:29:52ZMarek Szubaadd try::tiny*Created by: at7*
modules/Bio/EnsEMBL/IO/Parser.pm uses Try::Tiny*Created by: at7*
modules/Bio/EnsEMBL/IO/Parser.pm uses Try::Tinyhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/101102 testdb patches for variation2020-06-24T09:54:53ZMarek Szuba102 testdb patches for variation*Created by: ameya1981*
Test db patches for 102. variation db.*Created by: ameya1981*
Test db patches for 102. variation db.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/104add try::tiny2020-07-08T11:30:29ZMarek Szubaadd try::tiny*Created by: at7*
modules/Bio/EnsEMBL/IO/Parser.pm uses Try::Tiny*Created by: at7*
modules/Bio/EnsEMBL/IO/Parser.pm uses Try::Tinyhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/98e101 test db patch2020-03-17T15:08:47ZMarek Szubae101 test db patch*Created by: ameya1981*
Test DB Patching for 101.
No change in IO test cases.*Created by: ameya1981*
Test DB Patching for 101.
No change in IO test cases.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/96Patch test databases to schema version 1012020-01-21T12:09:01ZMarek SzubaPatch test databases to schema version 101*Created by: tgrego*
*Created by: tgrego*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/84README: Use the same badge syntax as for 'ensembl'2019-06-17T14:45:50ZMarek SzubaREADME: Use the same badge syntax as for 'ensembl'*Created by: mkszuba*
i.e. both Travis and Coveralls, explicitly specify the branch*Created by: mkszuba*
i.e. both Travis and Coveralls, explicitly specify the branchhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/88Travis: explicitly use Ubuntu Trusty for builds2019-06-25T12:08:02ZMarek SzubaTravis: explicitly use Ubuntu Trusty for builds*Created by: mkszuba*
## Use case
Make sure we are not affected by the ongoing change of the default Travis build environment from Ubuntu Trusty to Ubuntu Xenial, for which we are not ready yet, by explicitly requesting the former.
...*Created by: mkszuba*
## Use case
Make sure we are not affected by the ongoing change of the default Travis build environment from Ubuntu Trusty to Ubuntu Xenial, for which we are not ready yet, by explicitly requesting the former.
## Description
It has turned out that in spite of what the Travis documentation says, perl-5.14 is *not* available under the Xenial environment on Travis. We still require compatibility with that Perl version so it is necessary for us to make sure we continue to use Trusty even after the default Travis environment has been changed to Xenial, a change that is now in progress following the end of life of Ubuntu Trusty (see https://blog.travis-ci.com/2019-04-15-xenial-default-build-environment).
## Possible Drawbacks
Ubuntu Trusty has already reached end of life.
## Testing
_Have you added/modified unit tests to test the changes?_
No, changes affect Travis only.
_If so, do the tests pass/fail?_
N/A
_Have you run the entire test suite and no regression was detected?_
No, changes affect Travis only.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/95Yearly copyright update2020-01-21T12:08:42ZMarek SzubaYearly copyright update*Created by: tgrego*
This brings the copyright notices to the year 2020.*Created by: tgrego*
This brings the copyright notices to the year 2020.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/97[ENSCORESW-3106] BCF parser2020-01-21T14:27:19ZMarek Szuba[ENSCORESW-3106] BCF parser*Created by: tgrego*
This PR brings a BCF parser to ensembl-io.
BCF is a compiled version of VCF, thus a writer is not required because it is built by compiling existing VCF files (and a VCF writer is available).
For querying capa...*Created by: tgrego*
This PR brings a BCF parser to ensembl-io.
BCF is a compiled version of VCF, thus a writer is not required because it is built by compiling existing VCF files (and a VCF writer is available).
For querying capabilities an index of the .bcf file is required, this is a .bcf.csi file.
Testing is included and should be a good example of how to use the parser.
See ENSCORESW-3106 for more info.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/94[ENSCORESW-3334] escape RDF [release/99]2019-12-06T09:25:52ZMarek Szuba[ENSCORESW-3334] escape RDF [release/99]*Created by: tgrego*
backport of https://github.com/Ensembl/ensembl-io/pull/93*Created by: tgrego*
backport of https://github.com/Ensembl/ensembl-io/pull/93https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/92Patch test databases [master]2020-01-22T12:42:26ZMarek SzubaPatch test databases [master]*Created by: mkszuba*
Applies the core patch 99_100_b, and bumps the variation database all the way from schema version 96.*Created by: mkszuba*
Applies the core patch 99_100_b, and bumps the variation database all the way from schema version 96.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/93[ENSCORESW-3334] escape RDF2019-12-04T10:35:37ZMarek Szuba[ENSCORESW-3334] escape RDF*Created by: tgrego*
added an utf8 escape to avoid syntax errors on RDF.
URLs should be fine with the escape, and RDF will now be valid*Created by: tgrego*
added an utf8 escape to avoid syntax errors on RDF.
URLs should be fine with the escape, and RDF will now be validhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/100Changed badge to release/1022020-06-11T08:55:05ZMarek SzubaChanged badge to release/102*Created by: ameya1981*
Changed badge in readme to release/102*Created by: ameya1981*
Changed badge in readme to release/102https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/89Patch test databases to schema version 992019-09-16T12:42:33ZMarek SzubaPatch test databases to schema version 99*Created by: mkszuba*
Needed for today's branching.*Created by: mkszuba*
Needed for today's branching.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/99102 version bump, testdb patching2020-05-07T12:19:23ZMarek Szuba102 version bump, testdb patching*Created by: ameya1981*
Release related version bump and testdb patches*Created by: ameya1981*
Release related version bump and testdb patcheshttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/90Patch core and ontology test databases to schema version 1002019-11-06T10:56:39ZMarek SzubaPatch core and ontology test databases to schema version 100*Created by: mkszuba*
Part of the release cycle.
Some of the tests fail because they see unexpected "version mismatch" warnings, this should go away once ensembl#424 has been merged. With some luck other teams will have pushed their ...*Created by: mkszuba*
Part of the release cycle.
Some of the tests fail because they see unexpected "version mismatch" warnings, this should go away once ensembl#424 has been merged. With some luck other teams will have pushed their respective schema-version bumps by then and we'll be able to patch the variation test DB in the same PR.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/83ancestral_allele update2020-01-22T12:42:13ZMarek Szubaancestral_allele update*Created by: tgrego*
Variation `Bio::EnsEMBL::Variation::Variation::ancestral_allele` method has been deprecated and replaced with `Bio::EnsEMBL::Variation::VariationFeature::ancestral_allele`.
`Bio::EnsEMBL::IO::Translator::SampleGe...*Created by: tgrego*
Variation `Bio::EnsEMBL::Variation::Variation::ancestral_allele` method has been deprecated and replaced with `Bio::EnsEMBL::Variation::VariationFeature::ancestral_allele`.
`Bio::EnsEMBL::IO::Translator::SampleGenotypeFeature` uses the deprecated method and is now failing, so an update is required.
This fixes the issue by patching the test DBs and the test data object, and updated the deprecated method to the new one.