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add sample and dataset transfer/update (most cases), fix some issues #11

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merged 12 commits into from
Oct 15, 2024

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  • list-data now works as well when searching for samples
  • list-data now works when searching for identifiers (not only sample/experiment codes)
  • makes assay type mandatory for assay creation and adds helpful logging in case the properties file does not contain an assay type URI for the given experiment type. this is necessary as the API expects an assay type
  • enables config parameters to be overwritten by providing command line parameters
  • fixes recursion for list of parent properties. e.g. when listing datasets, more than one patient id will be shown, if more than one patient sample is part of the hierarchy
  • adds dataset type as option parameter for all commands creating datasets in openbis. default type is "UNKNOWN"
  • fixes issue introduced in the last snapshot, where the config would not be read in several of the older functions of the script
  • enables creation of samples and assets without creating an assay - for several cases this still needs rethinking, as the assay is the only connection between samples and assets
  • introduces short wait time (3 seconds) between assay and sample creation, as the script would sometimes fail at this point

@wow-such-code wow-such-code requested a review from a team as a code owner October 15, 2024 00:20
@wow-such-code wow-such-code merged commit e00052d into development Oct 15, 2024
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