Merge release/102 branch to master #299
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…o json to display as html through datacheck service
Fix typo in method name
…ies, the SQL in one test needs to be updated to count distinct versions, not seq_region names.
…ns of a particular coord_system are components, and others are unassembled top-level regions.
remove known phenotype descriptions
Fixes for two seq_region-related datachecks
…an updated meta_key
Detect assembly/geneset change
…t is not explicitly specified. This was being supplied in one part of this module (used by most datachecks), but not in another, when the registry is reloaded by a datacheck (as, for example, in a 'Compare*' datacheck that connect to the metadata database).
Fix for 'Compare*' datachecks in databases without species_id=1
…ayXrefExists for non-vertebrates. Reduce threshold for reporting differences with previous version, from 80% to 66% - too noisy otherwise, which makes it hard to spot significant problems.
Co-authored-by: Matthieu Muffato <muffato@ebi.ac.uk>
Co-authored-by: Matthieu Muffato <muffato@ebi.ac.uk>
Create new datacheck groups for xref-related pipelines.
species.db_name must be all lower-case
…eed to force the core database to be loaded into the registry (it's lazy-loaded, but for reasons that aren't clear, it isn't triggered as expected by the calls to the gene adaptor). This is not an issue when running within a pipeline, because the registry will automatically have been loaded in that case.
Force load of core db in GeneBiotypes, when run for core-like dbs
…database must be in the tested one
Missing homology MLSS check from PR #283
Missing MLSS checks from PR #292
length() is only useful to correct the length of circular slices when start is greater than end. Here start is guaranteed to be lower or equal than end. length() involves additional queries to get the seq_region_id and check whether the slice is circular.
… low memory footprint - Dnafrags too can be batched together. - This works for polyploid components too.
Cross-database compara datachecks + conflict resolution
Fix/compara dcs for e102
marcoooo
approved these changes
Sep 3, 2020
Pull Request Test Coverage Report for Build 1400
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