Refactor Import Automation #353
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…/github.com/microbiomedata/nmdc_automation into 332-issues-with-rerunning-import-automation
aclum
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Jan 31, 2025
aclum
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Jan 31, 2025
aclum
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Jan 31, 2025
| if object_type in ids: | ||
| return ids[object_type] | ||
| else: | ||
| workflow_obj_id = self.runtime_api.minter(object_type) + ".1" |
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this is missing logic check if should mint an new ID + .1 versus increment an existing ID
aclum
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Jan 31, 2025
| proj['apType'] in ["Metagenome Analysis", "Metatranscriptome Analysis"]] | ||
| else: | ||
| ap_type_gold_analysis_data = [] |
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consider making this an error @mflynn-lanl
aclum
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Jan 31, 2025
| data_generation_update_query['updates'].append(update) | ||
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| # Already has nmdc output | ||
| elif dg_output and dg_output[0].startswith('nmdc:dobj'): |
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This would be more robust if there was join on the data_object set record, making sure the 'name' of the data_object_set record matches what is in the import directory.
aclum
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Jan 31, 2025
aclum
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Jan 31, 2025
a data object is output by either a workflow execution or datq generation ID, both of with are planned processes
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This PR address the issues described in #332
providing a re-write of the import automation code.
The changes in project import behavior include:
json:validateendpointThe legacy activity_mapper package is replaced by a simplified import_mapper consisting of
The
import_projectscommand has been re-written to separate file mapping / file linking / and NMDC Database update operations.Additional Changes
tests/import_project_dirimport_mapperAdditional changes - not directly related to import