GitLab

ensemblgenomes-20-73'.

Sprout from master 2013-08-22 09:32:14 UTC Magali Ruffier <mr6@sanger.ac.uk> 'added fetch_stable_id_event and get_event methods for archivestableid, in adaptor and object modules respectively'
Cherrypick from master 2013-09-06 15:16:53 UTC Alessandro Vullo <avullo@ebi.ac.uk> 'Tests for subroutines in the Bio::EnsEMBL::Utils::IO module.':
    modules/t/io.t
    modules/t/test-genome-DBs/ontology/ontology/table.sql
    sql/patch_73_74_a.sql
    sql/patch_73_74_b.sql
    sql/patch_73_74_c.sql
    sql/patch_73_74_d.sql
    sql/patch_73_74_e.sql
    sql/patch_73_74_f.sql
Cherrypick from branch-ensembl-73 2013-08-30 09:06:03 UTC Magali Ruffier <mr6@sanger.ac.uk> 'revert changes for metacontainer support':
    misc-scripts/ontology/sql/patch_72_73_b.sql
    misc-scripts/ontology/sql/tables.sql
    modules/Bio/EnsEMBL/DBSQL/AssemblyAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
    modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
    modules/Bio/EnsEMBL/RepeatFeature.pm
    modules/Bio/EnsEMBL/Slice.pm
    modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm

added fetch_stable_id_event and get_event methods for archivestableid, in adaptor and object modules respectively
allows to get the specific event of an archive stable id related to a given stable id
finally gives access to score

with rest stack trace, \n is ignored and the query looks like columnFROM
it is not going to affect the running of the query, but can be confusing, so adding a space before the FROM

we have too many reg starting variables to use shortened names

replaced reg with registry for more explicit code

if we use first_registry and last_registry throughout the module, we can probably afford to use registry rather than reg for the simpler cases

Patch submitted by Leo for PGSQL default port number.

if your meta_coord table is wrong, you should run update_meta_coord.pl, not meta_levels.pl

After talking to Compara we found the need to support additional
lookups with the full id cache. Since all values are stored in memory
the lookup is very easy to compute.

Leo submitted patch. We support pgsql as a way of defining the driver. This
is inline with us accepting sqlite as a valid synonym for DBD::SQLite.

To provide improved querying of caches we now support SQL statements. These
queries return a list of keys (normally primary key db identifiers) defining
a list of objects to return. It is up to sub-BaseCache implementations to
deal with the nitty gritty of cache mis-hits (something they need to do
anyway).

The code previously allowed bogus numbers through into the final slice which
caused errors in later methods. The website crashed because of this. We will
reject anything that was not an integer if the start or end was defined.

Check feature out of destination slice. SimpleFeatureAdaptor debugged in the negative strand slice case

The big post-merge alt allele commit. Changes to alt_allele table, new tests, and a couple of new objects.

method to use is get_seq_region_id()

satisfies perl critic

we do not want to retrieve all symlinks of the slice, just the slice itself

eliminate the need for a specialised MiscFeature::new_fast implementation.

to provide correct comparison with initial seq_region_name, fetch the seq_region_name from the seq_region_id

do not attempt to ref object as it could be its id

for each object, methods are explicitly defined

[ENSCORESW-494]. IN statement is now generically handled rather than repeating the same logic over and over again

[ENSCORESW-478] and [ENSCORESW-467]. Brought in a Perl::Critic test being run on the lowest level. Tests are only run when we have the ENV TEST_AUTHOR is set to a true value. Otherwise it does not impact on the current test cases. Also had to fix a number of issues associcated with these flags. Mostly were due to not using warnings or strict. Anything I felt was ok or not my call has been annotated with a no critic flag.

[ENSCORESW-458]. _remap() (only used by KaryotypeAdaptor AFAIK) was not working. Used seq region names for commparisons when fastmap() returns seq region ids. Fixed to using just seq_region_ids. Issues originally raised by Steve S

[ENSCORESW-475] fixing the dbentry return to prioritise genes, transcripts and translations found on reference slices