Details
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Type:
Task
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Status: Resolved
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Priority:
Major
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 2.8
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Component/s: data retrieval services, Datamodel
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Labels:None
Description
This arose when fixing JAL-1062.
DAS source coordinate systems have a complex set of interrelationships. All Ensembl coordinate systems have their own URI, but the same authority string 'Ensembl' - which is what Jalview would normally use if it were to store the database name associated with a DAS source. However, in the 2.7 architecture, this results in a conflict, since Jalview uses the same 'DBName' string to lookup a particular SequenceFetcher for a database - and if multiple das sources have the same name, each one will overwrite the entry in Jalview's database fetcher registry for any previously registered 'Ensembl' sources.
In order to fix this, we need to generalise the registry to allow a new tier:
Top Tier: Primary authority { source 1 for authority, source 2 for authority, source 3 for authority }
- Jalview would then iterate through all sources for an authority, trying to retrieve each ID in turn.
DAS source coordinate systems have a complex set of interrelationships. All Ensembl coordinate systems have their own URI, but the same authority string 'Ensembl' - which is what Jalview would normally use if it were to store the database name associated with a DAS source. However, in the 2.7 architecture, this results in a conflict, since Jalview uses the same 'DBName' string to lookup a particular SequenceFetcher for a database - and if multiple das sources have the same name, each one will overwrite the entry in Jalview's database fetcher registry for any previously registered 'Ensembl' sources.
In order to fix this, we need to generalise the registry to allow a new tier:
Top Tier: Primary authority { source 1 for authority, source 2 for authority, source 3 for authority }
- Jalview would then iterate through all sources for an authority, trying to retrieve each ID in turn.