DO NOT MERGE 2414 change cardinality of was informed by to 1 to n #2422
Conversation
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| @@ -17,7 +17,8 @@ has_output: | |||
| img_identifiers: | |||
| - img.taxon:x1 | |||
| name: xxx | |||
| was_informed_by: nmdc:omprc-11-djb2d2 | |||
| was_informed_by: | |||
| - nmdc:omprc-11-djb2d2 | |||
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I noticed the number of spaces (4) used for indentation on the added line differs from the number (2) used for indentation elsewhere in the file. I recommend using the same number (2) as is already in use in the file.
I have the same comment about several of the example data files.
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I don't understand why these files were deleted from the repo:
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I recommend including at least one example data file in which there is more than one value in the |
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If I am understanding this schema change correctly (that the |
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@mbthornton-lbl Can we please add a description to |
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@eecavanna those are derived files and shouldn't be included or else we end up with a bunch of merge conflicts. |
aclum
changed the title
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Hi @aclum, it makes sense to me that they not be updated in this PR. The thing I'm confused about is why they are being deleted from the repo (as opposed to doing nothing) in this PR. |
I made was_informed_by globally multivalued so removing making it multivalued on WorkflowExecution
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I think the were accidentally added either here or with a previous PR |
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@eecavanna I am not sure how those files got deleted either :-/. I merged main back into this branch to restore them. |
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Pull Request Overview
This PR updates the cardinality of the "was_informed_by" field from a single scalar to a list, aligning the YAML examples and invalid test cases with the new specification. Key changes include:
- Converting scalar "was_informed_by" entries to list format across several YAML files.
- Updating valid and invalid example files to reflect the new multi-value pattern.
- Adding a new invalid example for a non-list "was_informed_by" value.
Reviewed Changes
Copilot reviewed 48 out of 49 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| src/data/invalid/MetaproteomicsAnalysis-invalid-missing-metap-cat.yaml | Changed scalar "was_informed_by" to a list |
| src/data/invalid/MetagenomeSequencing-bad_id_mention.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetagenomeSequencing-bad_id.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetagenomeAssembly-invalid-qc-status-rules.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetabolomicsAnalysis-metab_quantified.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetabolomicsAnalysis-invalid_id-4.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetabolomicsAnalysis-invalid_id-3.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetabolomicsAnalysis-invalid_id-2.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetabolomicsAnalysis-invalid_id-1.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetabolomicsAnalysis-invalid_execution_resource_not_in_enum.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetabolomicsAnalysis-invalid-missing_execution_resource.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/MetabolomicsAnalysis-invalid-has-slot-used.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/Database-metatranscriptome_workflow-invalidDatabase.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/Database-mags-img_identifiers-exceeds-cardinality.yaml | Reformatted "was_informed_by" as a list (in two spots) |
| src/data/invalid/Database-invalid_calibration_slot.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/Database-WorkflowExecutionActivity-invalid.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/Database-WorkflowExecution-was-informed-by-not-a-list.yaml | Introduced as a new invalid example with "was_informed_by" not in list format |
| src/data/invalid/Database-ReadQcAnalysisActivity-invalid.yaml | Reformatted "was_informed_by" as a list |
| src/data/invalid/Database-MetabolomicsAnalysis-no_metabolomics_category.yaml | Reformatted "was_informed_by" as a list |
Files not reviewed (1)
- nmdc_schema/gold-to-mixs.sssom.tsv: Language not supported
This PR provides:
multivalue: trueto the slot_usage for was_informed_byThis should not be merged until after the April 2025 release since this requires coordination with nmdc-server changes.