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Add a Sample grouping class in order to remove any_of range constraints #2244

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merged 4 commits into from
Dec 4, 2024
Merged

Add a Sample grouping class in order to remove any_of range constraints #2244

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b5a364e
add a 'Sample' grouping class in order to remove an_of range constraints
sierra-moxon Nov 1, 2024
8345e86
Merge branch 'main' into grouping_classes
sierra-moxon Nov 27, 2024
53e0120
fixed is_a hierarchy per code review
sierra-moxon Nov 27, 2024
93aba78
fix comment to disambiguate parent from ancestor
sierra-moxon Nov 27, 2024
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4 changes: 1 addition & 3 deletions src/schema/basic_classes.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -334,9 +334,7 @@ classes:
slot_usage:
has_input:
required: true
any_of:
- range: Biosample
- range: ProcessedSample
range: Sample
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
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17 changes: 11 additions & 6 deletions src/schema/core.yaml
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Expand Up @@ -217,6 +217,12 @@ classes:
syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$"
interpolated: true

Sample:
class_uri: 'nmdc:Sample'
description: A sample is a material entity that can be characterized by an experiment.
is_a: MaterialEntity
abstract: true


Biosample:
class_uri: 'nmdc:Biosample'
Expand Down Expand Up @@ -270,8 +276,9 @@ classes:
unique_keys:
samp_name_unique_key:
unique_key_slots:
- samp_name # id is already required to be unique because it is the identifier in Biosample's parent class, NamedThing
is_a: MaterialEntity
- samp_name # id is already required to be unique because it is the identifier
# in Biosample's ancestor class, NamedThing (parent is MaterialEntity)
is_a: Sample
in_subset:
- sample subset
aliases:
Expand Down Expand Up @@ -1219,9 +1226,7 @@ classes:
- This class is a replacement for BiosampleProcessing.
slot_usage:
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
range: Sample
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
Expand Down Expand Up @@ -1251,7 +1256,7 @@ classes:

ProcessedSample:
class_uri: nmdc:ProcessedSample
is_a: MaterialEntity
is_a: Sample
title: Processed Sample
slots:
- biomaterial_purity
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20 changes: 5 additions & 15 deletions src/schema/nmdc.yaml
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Expand Up @@ -399,9 +399,7 @@ classes:
slot_usage:
has_input:
required: true
any_of:
- range: Biosample
- range: ProcessedSample
range: Sample
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
Expand Down Expand Up @@ -546,9 +544,7 @@ classes:
mass:
description: The output mass of the SubSampling Process.
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
range: Sample
structured_pattern: # MAM 2024-05-22 isn't that inherited from a parent class?
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
Expand Down Expand Up @@ -581,9 +577,7 @@ classes:
structured_pattern:
syntax: "{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$"
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
range: Sample
structured_pattern: # MAM 2024-05-22 isn't that inherited from a parent class?
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
Expand Down Expand Up @@ -624,9 +618,7 @@ classes:
volume:
description: The volume of sample filtered.
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
range: Sample
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
Expand Down Expand Up @@ -684,9 +676,7 @@ classes:
structured_pattern:
syntax: "{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$"
has_input:
any_of:
- range: Biosample
- range: ProcessedSample
range: Sample
structured_pattern:
syntax: "{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$"
interpolated: true
Expand Down