Add datacheck CactusMetadataConsistency #560
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Description of the problem
Issues have arisen in recent releases with Cactus genomic alignment metadata consistency: in one case a retired
GenomeDBwas present in the HAL mapping which links a Compara database to its configured Cactus alignments, and in another case a species in the HAL mapping was not present in the corresponding species tree. Tickets have been created proposing to develop a datatcheck for each of these issues (ENSCOMPARASW-5088 and ENSCOMPARASW-6834, respectively).The datacheck which would be added by this PR tests both cases.
Scope of the pull request
This PR adds a Compara datacheck (
CactusMetadataConsistency) which tests that for each Cactus MLSS in a Compara database:genome_db_idin the HAL mapping is present in the database, is current, and can be found in the species tree.WARNING: like #557, this PR moves the CompareVariationRows datacheck index entry so that it is placed alphabetically.
Testing
The datacheck was tested successfully on 3 example Metazoa Compara databases. For further information on testing, please see ENSCOMPARASW-6834.