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

Using while shift will eventually cause an undef to be processed. This
is how the while loop detects a false condition. We cannot lc() an
undef. Do not do this in the while. Only do it in the loop

if biotypes between transcripts differ, add penalty
if biotype groups between transcripts differ, add even more penalty

allows to return protein feature specific attributes for translation rest endpoint

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

The method was called on the wrong object. Swithced around and tested

'logic_name' can be the analysis' logic_name, or the db name if nothing found
allows to fetch 'low_complexity' regions without knowing that the analysis is seg
only works if no protein_features were added to that translation
mimicks the webcode behaviour like in http://www.ensembl.org/Homo_sapiens/Transcript/Domains?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000544455

Nick in Ensembl Genomes has seen an issue with bacteria databases where
we exceed the number of connections on MySQL. As we loop through DBAdaptors
we do not disconnect. That means an ID which appears later on will have
opened all prior databases. The connection is still active. We now
disconnect this.

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

helps for consistency across modules
also makes it easier to grep for registry calls, reg is too generic (regulatory, region, registry...)

seq_regon_name would never have worked, so the warn would have ended up as a fail

Simple formatting changes suggested by Bron. Will make the example cut-paste
usable.

Patch submitted by Leo for PGSQL default port number.

We have decided to revert this change. GeneBuilder code has a link to the
existing functionality manifesting itself as subtle silent breakages. The
old functionality has been brought back. Warning added about how possibly
bad using the array from this function is.

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).

- seq: pass defined slice intervals to trigger the correct program flow in SequenceAdaptor
- project: removed since believed to have bugs
- project_org: removed since it's not used anywhere

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.

Nathan requested methods which can perform this kind of task (assert the contents
of a data structure). We support 1 level of arrays and hashes. All test cases
pass at time of writing. Methods for capturing method returns were
not implemented. They do not fit into the Utils way of doing (no method
actually performs a task on an object they just report what it is).

Removed get_all_ExternalFeatures method, now borrowed from parent where the corresponding adaptor handle the circular slice case