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Remove was_informed_by from WorkflowExecution and update data examples #30

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Dec 14, 2023
Merged

Remove was_informed_by from WorkflowExecution and update data examples #30

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1 change: 0 additions & 1 deletion src/data/invalid/Database-nom_analysis_set-incomplete-string-ended_at_time.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,4 +11,3 @@ nom_analysis_set:
type: xxx
started_at_time: "2018-11-111"
ended_at_time: "2018-11-13T20:20:39+00:00"
was_informed_by: nmdc:act-99-abcdefg
2 changes: 1 addition & 1 deletion src/data/invalid/Database-nom_analysis_set-non-string-ended_at_time.yaml
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Expand Up @@ -11,4 +11,4 @@ nom_analysis_set:
type: xxx
started_at_time: "2018-11-13T20:20:39+00:00"
ended_at_time: 2018-11-13T20:20:39+00:00
was_informed_by: nmdc:act-99-abcdefg

3 changes: 1 addition & 2 deletions src/data/invalid/Database-using-undefined-analytical_sample_set-slot.yaml
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@@ -1,5 +1,4 @@
analytical_sample_set: # slot not defined
- id: nmdc:ansm-99-dtTMNb
name: WOOD_024-M-20190715-COMP-DNA1
#is was_informed_by the right slot? The value of this slot should be the id from a PlannedProcess (ie extraction)
was_informed_by: nmdc:extr-1235

1 change: 0 additions & 1 deletion src/data/invalid/MetabolomicsAnalysisActivity-invalid-missing_execution_resource.yaml
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@@ -1,7 +1,6 @@
id: nmdc:wfmb-99-ABCDEF
started_at_time: '2021-08-05T14:48:51+00:00'
ended_at_time: '2021-09-15T10:13:20+00:00'
was_informed_by: nmdc:a1
git_url: https://example.org/WorkflowExecutionActivity
has_input:
- nmdc:i1
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1 change: 0 additions & 1 deletion src/data/invalid/MetabolomicsAnalysisActivity-invalid_execution_resource_not_in_enum.yaml
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@@ -1,7 +1,6 @@
id: nmdc:wfmb-99-ABCDEF
started_at_time: '2021-08-05T14:48:51+00:00'
ended_at_time: '2021-09-15T10:13:20+00:00'
was_informed_by: nmdc:a1
execution_resource: NERSC - Cori
git_url: https://example.org/WorkflowExecutionActivity
has_input:
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3 changes: 0 additions & 3 deletions src/data/invalid/MetagenomeSequencing-bad_id.yaml
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Expand Up @@ -12,9 +12,6 @@ version: v1.0.0
# or referential integrity violations
has_output:
- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3
# legacy was_informed_by id? validator won't catch pattern violations
# or referential integrity violations
was_informed_by: gold:Gp0213371
name: Sequencing Activity for nmdc:mga0vx38
started_at_time: '2021-08-05T14:48:51+00:00'
ended_at_time: '2021-09-15T10:13:20+00:00'
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3 changes: 0 additions & 3 deletions src/data/invalid/MetagenomeSequencing-no_parthood.yaml
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Expand Up @@ -11,9 +11,6 @@ version: v1.0.0
# or referential integrity violations
has_output:
- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3
# legacy was_informed_by id? validator won't catch pattern violations
# or referential integrity violations
was_informed_by: gold:Gp0213371
name: Sequencing Activity for nmdc:mga0vx38
started_at_time: '2021-08-05T14:48:51+00:00'
ended_at_time: '2021-09-15T10:13:20+00:00'
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1 change: 0 additions & 1 deletion src/data/invalid/NomAnalysisActivity-remove_used.yaml
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Expand Up @@ -12,5 +12,4 @@ nom_analysis_activity_set:
type: nmdc:NomAnalysisActivity
started_at_time: "2018-11-13T20:20:39+00:00"
ended_at_time: "2018-11-13T20:20:39+00:00"
was_informed_by: nmdc:act-99-abcdefg
used: 12T_FTICR_B
24 changes: 24 additions & 0 deletions src/data/invalid/ReadQCAnalysis-invalid-has-was_informed_by.yaml
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@@ -0,0 +1,24 @@
id: nmdc:wfrqc-99-ABCDEF
ended_at_time: '2021-09-15T10:13:20+00:00'
execution_resource: NERSC-Perlmutter
git_url: git_url1
input_base_count: 300.0
input_read_bases: 300.0
input_read_count: 10.0
name: name1
output_base_count: 100.0
output_read_bases: 100.0
output_read_count: 3.0
started_at_time: '2021-08-05T14:48:51+00:00'
type: type1
part_of: "nmdc:wfch-11-ab"
was_informed_by: "nmdc:wfch-99-qwertyuiop"
has_input:
- "jgi:534819030d87850d7aea2a16"
has_output:
- "nmdc:ae40d7ae535c92b6d347915d8b1ac125"
- "nmdc:bd723452a107e973fcc6734ff7894bb9"
#part_of:
#used: used1
#version: version1
#was_associated_with:
1 change: 0 additions & 1 deletion src/data/valid/Database-MetabolomicsAnalysis-1.yaml
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Expand Up @@ -3,7 +3,6 @@ metabolomics_analysis_set:
name: Metabolomics Analysis Activity for nmdc:wfmb-99-ABCDEF
started_at_time: '2021-08-05T14:48:51+00:00'
ended_at_time: '2021-09-15T10:13:20+00:00'
was_informed_by: nmdc:a1
execution_resource: NERSC-Cori
part_of: nmdc:wfch-11-ab
git_url: https://example.org/WorkflowExecutionActivity
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