Rework plate naming priorities so that reader-supplied names can be used #2
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The user specified name is typically non-null, even if the user did not explicitly enter a plate name. This attempts to distinguish between "real" user specified names and default names based upon the imported file name. The default names appear to come from ome.formats.importer.ImportFixture, but changes were not made there so as to not affect non-SPW imports.
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See also discussion here: ome/design#57 |
This removes the automatic setting of user-specified names in the importer, so that later calls to retrieve the user-specified name are guaranteed to return only what the user actually specified (or null by default). Plate and Image names supplied by the reader are trusted when the user has not specified a name. The name(s) will be set to the relative path of the imported file only if both the user- and reader-specified names are null. The issue of 255 character limits on name fields has not been addressed here, but a comment has been added so that it's easier to go back to later.
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This is one attempt at resolving the long-standing issue of reader-supplied plate names being overwritten by the name of the imported file (which is set as the user specified name). The default names appear to come from ome.formats.importer.ImportFixture, but changes were not made there so as to not affect non-SPW imports.
Changes here were written and tested in the context of Harmony work, but all plate imports will be impacted. I would expect
bin/omero import -n TestPlateName Images/Index.idx.xmlto result in the same plate name (TestPlateName) with and without this change.bin/omero import Images/Index.idx.xmlresults in a plate namedIndex.idx.xmlwithout this, and should result in a plate named according to theNametag underPlatein theIndex.idx.xmlfile.