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Feature/remove unused reference databases#46
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SolomonShorser-OICR merged 15 commits intodevelopfrom May 5, 2017
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Improved error handling/logging for ENSEMBL file processor and BRENDA file retriever - and cascading changes to AddLinks. Also, fixed some logic related to creating ENSEMBL references - it was not getting the correct list of ReferenceDatabase DB_IDs.
reference-databases.xml
- If an identifierValue gets into the ReferenceCreator and the target DB is a KEGG db, then any species code prefix must be removed. - If the referred-to-object has a geneName, add it to the Identifier so that the _displayName can include it (that logic happens deep inside the reactome library).
- capture BRENDA result (facepalm!) - ENSEMBL file retrievers won't print a "missing ratelimit" message if they are not hitting the main ENSEMBL REST server. - remove logging statement. - update flybase URL - ignore diffReport files.
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Remove unused ReferenceDatabase objects, and a whole bunch of other small fixes: