JEnsembl: Change Log
2015-01-13
Release of API version 1.78 and Configuration module 1.78 (Download Binaries).
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.78</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.78</version>
</dependency>
- Configuration Change
- Recognizes Ensembl schema version 78. Introduced searching for partial matches on species aliases/names (to assist searching amongst similarly named bacterial species/strains).
- API
- SVN commits 572-577.
- Added a robots.txt file to webapp.
- Provided 'begins with' and 'contains' searching of aliases: added registry methods to allow searching for Species by partial aliases. The implementation differs for bacterial_oldstyle and bacterial_newstyle databases.
- In release 24/77 bacterial genomes drop species.common_name, species.ensembl_alias_name, species.short_name. Adapt parsing of species properties to fill in these values with species.display_name.
- Protect against 'Version' paramaterized queries of Collection Species (i.e. becteria). Since only one release of bacterial genomes can be loaded to a registry it no longer makes sense to parameterize a query with the version number - as any non-loaded version value will return null or empty. Various unit and functional tests updated to account for this change - i.e RuntimeExceptions thrown by inappropriate queries.
2014-08-27
Release of API version 1.76 and Configuration module 1.76 (Download Binaries).
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.76</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.76</version>
</dependency>
- Configuration Change
- Recognizes Ensembl schema version 76. Data access API modifications reflect some significant changes to the Compara schema regarding storage of gene homologies, new HomologyTypes and additional homology score information added to Gene model.
- API
- SVN commits 560-566.
- Changes to compara schema, 'member' table replaced by 'gene_member' and 'seq_member': required changes to sql to retrieve gene homologies.
- Changes to HomologyType enumeration, including the new Homoeologue relationship (for intraspecific relationships between Wheat chromosomes). 2 new HomologyTypes classify changes to genes in Homo sapiens assembly patches as projection_unchanged/altered.
- Modified Gene model to have homology counts and the DAO routines to fill these in on initialization or re-initialisation.
- Updates all functional tests in EnsemblTest module so that it works with new schema of version 76 in particular concentrated on ensuring bacterial collections working ok added a new class to look at the Homology counts on a Gene.
2014-03-17
Release of API version 1.75 and Configuration module 1.75 (Download Binaries).
NOTE: API release version jump from 1.19 to 1.75 to match Configuration release version.
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.75</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.75</version>
</dependency>
- Configuration Change
- Recognizes Ensembl schema version 75. No consequential changes to data mappings.
- API
- SVN commits 540-548.
- Changed DBRegistry to act as a factory capable of providing instances of itself.
- Creation of 'Uninitialized' DBRegistries allows for query of available releases at a Data Source without lengthy load/parsing of the entire resource.
- Alternate methods for DBRegistry creation now allow database loading to be restricted to specific release (or current) versions of the Data Source. This change is important for the efficient loading of Registries (i.e. parsing the available databases) with the increasing scale of Data Sources (particularly EnsemblGenomes).
- Introduced new separate DataSource configuration type 'ENSEMBLBACTERIA'; allows separate JEnsembl connection to EnsemblGenomes or EnsemblBacteria (or Ensembl Vertebrates).
- Fixed bug with previous check-in failing to load pan_homology databases.
- Updated some tests.
- Minor reorganizion of Maven dependency inheritance (for testing).
2014-01-03
Release of API version 1.19 and Configuration module 1.74 (Download Binaries).
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.19</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.74</version>
</dependency>
- Configuration Change
- Recognizes Ensembl schema version 74.
- Removal of the canonical_annotation column in the gene table, as it is not used any more.
- the 'subtype' column in homology has to been dropped in favour of the 'species_tree_node_id'. (Changed the query getHomologiesForGene in v74 compara configuration)
- API
- SVN commits 524-538.
- Ensembl Genomes have rationalised some of their species aliases - where they were ambiguous - e.g. they stop using 'rice' for O.sativa.... therefore some of the functional tests in EnsemblTest module needed tweaked.
- There are other alias issues - causing the return of some non-unique exceptions on searches. Improved how these are handled, to suggest how to list an appropriate database name
- Maven was failing to run JUnit tests in the EnsemblTest module correctly - so moved these to be functional tests...
- Some work on Registry initialization started, in order to make it configureable, to handle the increasing scale of EnsemblGenomes resources.
2013-07-12
Release of API version 1.18 and Configuration module 1.72 (Download Binaries).
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.18</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.72</version>
</dependency>
- Expanded XRefs and GOEvidence, (using Codes) for XRefs that hold GO terms. Filled in JUnit tests for the DataAccess layer. Alterred DAVariationXref - it has no factory so is not really 'datasource aware'. Fixed a bug in reinitialization by lazyload for DAGene.
2013-05-30
Sourceforge repository has been moved!
Read-only checkout:
svn checkout svn://svn.code.sf.net/p/jensembl/code/ yourDir. Browsable Web access is at http://sourceforge.net/p/jensembl/code/.
Note that the svn+ssh access protocol is now supported & rewuired for commiting to the repository (only allowed for registered developers).
2013-05-01
Release of API version 1.17 and Configuration module 1.71 (Download Binaries).
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.17</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.71</version>
</dependency>
- 477-480: changes to species look up by alias - to account for the possiblity of aliases being non-unique. (There are particular problems with resolving bacterial species across database releases in versions prior to EG 16, which intorduced use of the unique ENA GC Accession identifiers).
2013-03-05
Release of API version 1.16 and Configuration module 1.70.2 (Download Binaries).
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.16</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.70.2</version>
</dependency>
- 449-458: Changes to handling of (bacterial) CollectionSpecies to reflect changes in data organisation in EnsemblGenomes release 17. Storage of Database-styleSpeciesName, ComparaName, AssemblyAccession and AssemblyName for Species are now 'version aware' and bacterial species identity is established via the AssemblyAccession. From Release 17 bacterial homologies are accessd from the Pan Homology database. The classification of CoordinateSystems now identifies the lowest ranked (default-type) CS for a Species as the primary (top) view level - whether or not this Rank=1, and independent of the CS type (chromosome, supercontig.... etc).
- 451: Bug fix for querying whether a DatasourceAware Chromosome hasExceptions/Patches.
- 448: Bug fix for JUnit testing DataAccess package.
- 447: Minor bug minor fixes to some functional tests against current releases ensembl70/genomes17.
- 446: Change logic controlling lazyloading of DAObjects.
- 445: Tidying up Maven build: to get rid of warnings, reorganize javadoc/sources plugins, update licence headers.
2013-01-21
Release of API version 1.15 and Configuration module 1.70 (Download Binaries).
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.15</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.70</version>
</dependency>
- 432-433: Re-organized XRef methods etc., and now store a per database cache of ExternalDBs.
- 428-429: added ability to retrieve a CCDS ID(s) ( and XRef(s) ) for a Transcript. (These are displayed as the value of the display_id not primary_accession, as this include a .version number...). Also ability to fetch a transcript by a CCDS ID.
- 426-427: Introduced ability to get list of genes by synonym or name, and to get lists of synonyms for genes (via their xrefs).
- 408, 411-418, 421-422: added ability to fetch VegaIDs for Transcripts, Translations and Genes; and to get these objects for a given VegaID.
- 407, 421-422: Added Analysis Object to the model and DAO infrastructure - so far used by exon, transcript and gene. Tidied up reinitialization code used for lazyloading missing key properties for these objects (the initial get Gene/Exon/Transcript queries now set these objects to 'initialized' to prevent lazyload loops).
- 404-405: implemented a second HomologyDAO method and query for getting homologies and mappings for a given target species for all the genes lying on a source chromosome region, but allowing filtering on a target chromosome name. This may speed up the query - and should often make the result set much smaller, speeding up the processing of results. This method would be called where a user already know which homologous chromosome they wish to investigate. Note the query has been optimized to run as fast as possible - making it more lightweight (by not getting all homology information) does not speed up significantly.
2012-10-23
Release of API version 1.14 and Configuration module 1.69 (Download Binaries).
Maven Dependencies (see explanation)
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-data-access</artifactId>
<version>1.14</version>
</dependency>
<dependency>
<groupId>uk.ac.roslin</groupId>
<artifactId>ensembl-config</artifactId>
<version>1.69</version>
</dependency>
- 372-383 Worked up the chromosome/gene/transcript (primary and processed)/exon/translation/protein axes to interlink and provide methods to convert positions between all of these axes (see description).
- 364-371 Expanded sequence and RNA sequence methods of DAFeatures and Assemblies. Disallow use of position '0' (zero) - throws runtime illegal argument exception. Add new runtime exception 'RangeException' for invalid ranges. Add 'Padded' methods to append/prepend unknown nucleotides.
- 362 Rationalized use of logging and JUnit Test/Mock dependencies
- 361 Handling database rename from pongo_pygmeus to pongo_abelii in version 62
- 358-360 Added functionality to get top level fragments. In order to display 'Chromosome Fragments' where no chromosomes have been assigned in a given genome assembly.