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update existing seek nodes and fix stuff #9

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merged 1 commit into from
Oct 11, 2024

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  • allow update of existing assays in SEEK (found via openBIS identifier) and their samples and attached assets
  • inform user adding sample-types from openbis to SEEK, if they already exist and don't add them a second time. can be ignored via command line option
  • do not create blobs for assets in SEEK, if the user only want to link to openBIS
  • fix issue where SEEK authentication was asked of the user even if only openBIS commands were used
  • fetch all patient ids that are connected to a selected dataset (instead of only the first one found)
  • attempt to fix "NotFetchedException: Parents have not been fetched." problem by setting fetch options for more hierarchy levels
  • move a number of mappings for openBIS==>SEEK to their own property files that can be edited by the user
  • add parameters for project and study in SEEK
  • add a number of parameters to the config file:
    ** seek_default_project
    ** seek_default_investigation
    ** seek_openbis_sample_title (name of the property to be created/used in SEEK sample types to reference the openBIS identifier)

@wow-such-code wow-such-code requested a review from a team as a code owner October 11, 2024 14:44
@wow-such-code wow-such-code merged commit b9a6f20 into development Oct 11, 2024
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