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feat: refactor suspension type validation logic to be simpler and mor…
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…e performant (#1155)
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@nayib-jose-gloria
nayib-jose-gloria authored Dec 16, 2024
1 parent c2f4979 commit ee393cd
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286 changes: 75 additions & 211 deletions cellxgene_schema_cli/cellxgene_schema/schema_definitions/schema_definition.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,12 @@ components:
type: curie
dependencies:
- # If tissue_type is tissue OR organoid
rule: "tissue_type == 'tissue' | tissue_type == 'organoid'"
rule:
column: tissue_type
match_exact:
terms:
- tissue
- organoid
error_message_suffix: >-
When 'tissue_type' is 'tissue' or 'organoid',
'tissue_ontology_term_id' MUST be a descendant term id of 'UBERON:0001062' (anatomical entity).
Expand All @@ -199,7 +204,11 @@ components:
UBERON:
- UBERON:0001062
- # If tissue_type is cell culture
rule: "tissue_type == 'cell culture'"
rule:
column: tissue_type
match_exact:
terms:
- cell culture
error_message_suffix: >-
When 'tissue_type' is 'cell culture', 'tissue_ontology_term_id' MUST be either a CL term
(excluding 'CL:0000255' (eukaryotic cell), 'CL:0000257' (Eumycetozoan cell),
Expand All @@ -222,7 +231,11 @@ components:
type: curie
dependencies:
- # If organism is Human
rule: "organism_ontology_term_id == 'NCBITaxon:9606'"
rule:
column: organism_ontology_term_id
match_exact:
terms:
- NCBITaxon:9606
error_message_suffix: >-
When 'organism_ontology_term_id' is 'NCBITaxon:9606' (Homo sapiens),
self_reported_ethnicity_ontology_term_id MUST be formatted as one
Expand Down Expand Up @@ -285,7 +298,11 @@ components:
type: curie
dependencies:
- # If organism is Human
rule: "organism_ontology_term_id == 'NCBITaxon:9606'"
rule:
column: organism_ontology_term_id
match_exact:
terms:
- NCBITaxon:9606
error_message_suffix: >-
When 'organism_ontology_term_id' is 'NCBITaxon:9606' (Homo sapiens),
'development_stage_ontology_term_id' MUST be the most accurate descendant of 'HsapDv:0000001' or unknown.
Expand All @@ -300,7 +317,11 @@ components:
exceptions:
- unknown
- # If organism is Mouse
rule: "organism_ontology_term_id == 'NCBITaxon:10090'"
rule:
column: organism_ontology_term_id
match_exact:
terms:
- NCBITaxon:10090
error_message_suffix: >-
When 'organism_ontology_term_id' is 'NCBITaxon:10090' (Mus musculus),
'development_stage_ontology_term_id' MUST be the most accurate descendant of 'MmusDv:0000001' or unknown.
Expand Down Expand Up @@ -353,227 +374,70 @@ components:
selected the most appropriate value for the assay(s) between 'cell', 'nucleus', and 'na'. Please contact [email protected]
during submission so that the assay(s) can be added to the schema definition document.
dependencies:
- # If assay_ontology_term_id is EFO:0030080 or its descendants, 'suspension_type' MUST be 'cell' or 'nucleus'
complex_rule:
match_ancestors:
column: assay_ontology_term_id
- # 'suspension_type' MUST be 'cell' or 'nucleus'
rule:
column: assay_ontology_term_id
match_ancestors_inclusive:
ancestors:
EFO:
- EFO:0030080
inclusive: True
- EFO:0030080
- EFO:0010184
match_exact:
terms:
- EFO:0010010
- EFO:0008722
- EFO:0010550
- EFO:0008780
- EFO:0700010
- EFO:0700011
- EFO:0009919
- EFO:0030060
- EFO:0022490
- EFO:0030028
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0030080 or its descendants
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0007045 or its descendants, 'suspension_type' MUST be 'nucleus'
complex_rule:
match_ancestors:
column: assay_ontology_term_id
- # 'suspension_type' MUST be 'nucleus'
rule:
column: assay_ontology_term_id
match_ancestors_inclusive:
ancestors:
EFO:
- EFO:0007045
inclusive: True
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0007045 or its descendants
enum:
- "nucleus"
- # If assay_ontology_term_id is EFO:0010184 or its descendants, 'suspension_type' MUST be 'cell' or 'nucleus'
complex_rule:
match_ancestors:
column: assay_ontology_term_id
ancestors:
EFO:
- EFO:0010184
inclusive: True
- EFO:0007045
- EFO:0002761
match_exact:
terms:
- EFO:0008720
- EFO:0030026
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0010184 or its descendants
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0008994 or its descendants, 'suspension_type' MUST be 'na'
complex_rule:
match_ancestors:
column: assay_ontology_term_id
- #'suspension_type' MUST be 'cell'
rule:
column: assay_ontology_term_id
match_ancestors_inclusive:
ancestors:
EFO:
- EFO:0008994
inclusive: True
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008994 or its descendants
enum:
- "na"
- # If assay_ontology_term_id is EFO:0008919 or its descendants, 'suspension_type' MUST be 'cell'
complex_rule:
match_ancestors:
column: assay_ontology_term_id
ancestors:
EFO:
- EFO:0008919
inclusive: True
- EFO:0008919
match_exact:
terms:
- EFO:0030002
- EFO:0008853
- EFO:0008796
- EFO:0700003
- EFO:0700004
- EFO:0008953
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008919 or its descendants
enum:
- "cell"
- # If assay_ontology_term_id is EFO:0002761 or its descendants, 'suspension_type' MUST be 'nucleus'
complex_rule:
match_ancestors:
column: assay_ontology_term_id
- # 'suspension_type' MUST be 'na'
rule:
column: assay_ontology_term_id
match_ancestors_inclusive:
ancestors:
EFO:
- EFO:0002761
inclusive: True
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0002761 or its descendants
enum:
- "nucleus"
- # If assay_ontology_term_id is EFO:0010010, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0010010'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0010010
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0008720, 'suspension_type' MUST be 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0008720'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008720
enum:
- "nucleus"
- # If assay_ontology_term_id is EFO:0008722, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0008722'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008722
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0030002, 'suspension_type' MUST be 'cell'
rule: "assay_ontology_term_id == 'EFO:0030002'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0030002
enum:
- "cell"
- # If assay_ontology_term_id is EFO:0008853, 'suspension_type' MUST be 'cell'
rule: "assay_ontology_term_id == 'EFO:0008853'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008853
enum:
- "cell"
- # If assay_ontology_term_id is EFO:0030026, 'suspension_type' MUST be 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0030026'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0030026
enum:
- "nucleus"
- # If assay_ontology_term_id is EFO:0010550, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0010550'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0010550
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0008796, 'suspension_type' MUST be 'cell'
rule: "assay_ontology_term_id == 'EFO:0008796'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008796
enum:
- "cell"
- # If assay_ontology_term_id is EFO:0700003, 'suspension_type' MUST be 'cell'
rule: "assay_ontology_term_id == 'EFO:0700003'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0700003
enum:
- "cell"
- # If assay_ontology_term_id is EFO:0700004, 'suspension_type' MUST be 'cell'
rule: "assay_ontology_term_id == 'EFO:0700004'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0700004
enum:
- "cell"
- # If assay_ontology_term_id is EFO:0008780, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0008780'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008780
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0008953, 'suspension_type' MUST be 'cell'
rule: "assay_ontology_term_id == 'EFO:0008953'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008953
enum:
- "cell"
- # If assay_ontology_term_id is EFO:0700010, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0700010'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0700010
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0700011, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0700011'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0700011
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0009919, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0009919'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0009919
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0030060, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0030060'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0030060
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0022490, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0022490'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0022490
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0030028, 'suspension_type' MUST be 'cell' or 'nucleus'
rule: "assay_ontology_term_id == 'EFO:0030028'"
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0030028
enum:
- "cell"
- "nucleus"
- # If assay_ontology_term_id is EFO:0008992, 'suspension_type' MUST be 'na'
rule: "assay_ontology_term_id == 'EFO:0008992'"
- EFO:0008994
match_exact:
terms:
- EFO:0008992
type: categorical
error_message_suffix: >-
when 'assay_ontology_term_id' is EFO:0008992
enum:
- "na"
tissue_type:
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