Skip to content

mslibrary-databases.md

Latest commit

 

History

History
13 lines (10 loc) · 1.21 KB

mslibrary-databases.md

File metadata and controls

13 lines (10 loc) · 1.21 KB
Raw

Using databases created by MSLibrary

MetaPhoenix was previously named MSLibrary. Databases created with MSLibrary, including the mslibrary database used for the paper, can be used as they are without migration:

export MONGODB_URI=mongodb://localhost:27017/mslibrary
  • Documents written by MSLibrary store their Java type as _class: net.csibio.mslibrary.*. MetaPhoenix maps these to the current net.csibio.metaphoenix.* classes when reading (see LegacyTypeInformationMapper). Documents written from now on use the new class names, and old and new documents can live in the same collection.
  • Collection names (spectrum-<libraryId>, spectrum-<libraryId>-<DecoyStrategy>, library, ...) are unchanged.
  • Statistics are still stored under the key MSLibraryCompoundNum so that existing stat documents stay readable.
  • To analyse an old database without changing it, also start with --spring.data.mongodb.auto-index-creation=false. Otherwise Spring creates any missing indexes at startup. Commands such as filter and decoy write to the database.
  • If Redis caching is enabled, flush the cache once after upgrading. Cached entries store class names under the old package and cannot be read by the new code.