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molgenis / molgenis-tools-emx-downloader

Stand alone tool to download data in EMX format from molgenis servers
GNU Lesser General Public License v3.0
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Downloader creates Excel sheets for the sys_md_* tables when downloading the Negotiator configuration #59

Open esthervanenckevort opened 6 years ago

esthervanenckevort commented 6 years ago

When downloading the Negotiator Configuration entities, which refer to entities and attributes in the metadata the sysmd* tables are also added to the sheets. This is not desirable, and these entities should be ignored as data.

marikaris commented 6 years ago

This is just how the EMX downloader works. All references in the table you want to download should be downloaded when downloading data and metadata right?

Especially when downloading a system entityType I don't think it's weird that referenced system entities are downloaded as well, when we disable the downloading of referenced sys entityTypes, also the Negotiator Configuration Attributes are not downloaded anymore and that's also not what you want I think (and if so, you could of course also download without metadata)

esthervanenckevort commented 6 years ago

The entities in sys_md package are in my opinion an exception, since they represent the entities. The entities are serialized in a different way in EMX. In the original code I filtered out these entities.

marikaris commented 6 years ago

Ok, I will discuss this with the others