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Prototype automation
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update-study does not update omics_processing.has_input #135

Closed mbthornton-lbl closed 2 months ago

mbthornton-lbl commented 2 months ago

example

{
"_id": {
"$oid": "649b009773e8249959349b33"
},
"id": "nmdc:omprc-11-0mma7r06",
"name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
"description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
"has_input": [
"gold:Gb0115217"
],
"has_output": [
"jgi:55d740280d8785342fcf7e39"
],
"part_of": [
"nmdc:sty-11-aygzgv51"
],
"add_date": "2015-05-28",
"mod_date": "2021-06-15",
"ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
"omics_type": {
"has_raw_value": "Metagenome"
},
"principal_investigator": {
"has_raw_value": "James Stegen"
},
"processing_institution": "JGI",
"type": "nmdc:OmicsProcessing",
"gold_sequencing_project_identifiers": [
"gold:Gp0115663"
]
}
aclum commented 2 months ago

The issue is in line 227 of re_id_tool.py where a legacy biosample ID was being set with the biosample.id variable