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NAL-i5K / tripal_eutils

ncbi loader via the eutils interface
GNU General Public License v3.0
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Issue #256 detect if not public #257

Closed dsenalik closed 1 year ago

dsenalik commented 1 year ago

Issue #256

This adds some additional validation to detect the case where a linked record may not yet be publicly released.

Example using this pull request

INFO (TRIPAL_EUTILS): Inserting record into Chado: biosample: 18220869 (SAMN18220869)
Inserting record into Chado: biosample: 18220869 (SAMN18220869)
INFO (TRIPAL_EUTILS): Linking pre-existing organism 79196
Linking pre-existing organism 79196
ERROR (TRIPAL_EUTILS): Cannot fetch NCBI record: bioproject : 708186
[site http://default] [TRIPAL ERROR] [TRIPAL_EUTILS] Cannot fetch NCBI record: bioproject : 708186
ERROR (TRIPAL_EUTILS): ERROR Could not make request: The following ID is not public in BioProject: 708186
[site http://default] [TRIPAL ERROR] [TRIPAL_EUTILS] ERROR Could not make request: The following ID is not public in BioProject: 708186
ERROR Could not make request: The following ID is not public in BioProject: 708186
[site http://default] [TRIPAL ERROR] [TRIPAL_JOB] ERROR Could not make request: The following ID is not public in BioProject: 708186