GitLab

is_canonical() can lazy-load the value from the database when it is unset & a dbID and an adaptor is available.

toplevel location code can now deal with excessively large regions and shrinks them down to size if possible or rejects them.

in the ananlysis table, return a reference to an empty list.  Without
this change, all features would have been returned which would quickly
make the client run out of memory.

added fetch_all_by_name which gets all the xrefs that have the accession, display_label or synonym that is passed to it. external database source is optional

Functionality suggested by Ensembl Genomes, used when building a variation DB.
New flag: start_equals_end which controls the simplified sql for 1bp slice.

Bringing in the DataFile infrastructure. First pass implementation can perform CRUD and has associated test cases. Currently lacks a good way of passing the base directory in. Will be addressed.

Bringing in a new method which allows us to retrieve the last inserted identifier into the table this adaptor is working with via DBI. Should be called from within an execute block so we do not need to wrap this in a work_with_dbh call

Brought in a new method for getting single value meta items from the meta table. This is then used in MetaContainer for just about every call reducing duplicated logic.

Moved the warning about the cache not being on back into the constructor & simplified the construction method for the cache. If someone doesn't inherit from this correctly they'll loose the warning but that is all.

Brought in new_fast() as a speed increase.  Should probably consider moving new_fast() up to Storable.pm to give it to as many modules as possible & reduce code duplication

Caches are now created from an accessor rather than building them in the new(). This allows us to remove the new() and lets people inherit from here however they want to. It also stops us from auto-vivifying a plain hash which causes unintentional object retention.

clear_cache() did not de-reference the hash before clearning which could have caused the same situation of creating an auto-vivified hash.

Regression test put in place to stop this from happening again.

Adding a global here to allow for silencing of the no_cache warning. Important for dump applications where caching is not that useful

Use seq_region mappings correctly by getting all external seq_region_ids
for our internal seq_region_id and then using an IN-list in the
subsequent query.

DBNAME is no longer a required attribute as we now allow for direct DB connections. SQLHelper is now an attribute of a DBConnection. Methods added to avoid unintentional DB disconnections, working with the DBH safely and quote DB identifiers if required (useful to avoid SQL injection attacks with auto-generated code). Equals method also improved. Associated test cases written.

db_name in external_db. Clean up a few bugs while I'm at it.

Bugs corrected:

  A list (rather than a list reference) was returned if the
  external_db_id for the given db_name could not be found.

  The list returned from list_gene_ids_by_external_db_id() (in
  DBEntryAdaptor) was used as a hash.

For release 64 we've found that features on human HSCHR5_1_CTG1 would
not get fetched since its seq_region_id is an internal_seq_region_id
with a corresponding, but non-existent, external_seq_region_id in the
seq_region_mapping table.

Previous change backed out, as not in all cases 1bp slice start = seq_region_start or slice end = seq_region_end.