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  • v6.1RC5 - missing specimen type

    #1

    I’m missing specimen types in a fresh install of openspecimen v6.1RC5. Only PBMC and buffy coat are shown in the specimen type dropdown.
    image

    The majority of specimen types are defined in db v2.0 in the specimen-class-and-type.csv file. PBMC and buffy coat appear to be added/modified in higher versions. Checking the logs I saw that the precondition check for the import of specimen class and type fails.


    In consequence the data got never imported?

    I think the problem was introduced with the commit https://github.com/krishagni/openspecimen/commit/fd26e8c5fec2638e7011ae4bd17769a03d609b62, more specifically in be7270a. Parent classes and types were separated into two files, but the precondition used to check if the file is to be imported is for both the same. After the import of specimen-class.csv entries with the public_id 2003991 already exist and the additional specimen-class-and-type.csv files does not get imported.

    #2

    Hi @Andreas_Heinzel

    Thanks for reporting the issue. We’ll look into this issue and perhaps fix this in v6.1.RC6.

    Thanks,
    Vinayak

    #3

    Hi @vpawar,

    thank you for your reply.

    Would be great to see this fixed in RC6 as it is quite a bumper for people starting from scrach (empty database).

    I created a pull request that should hopefully save you some work.

    Best,
    Andreas

    #4

    Hi @Andreas_Heinzel

    We’ve fixed this issue in v6.1.RC6 build. Many thanks for reporting the issue and sharing your thoughts.

    Thanks,
    Vinayak