Skip to content

Update to clinical-microschemas v0.0.8 and fix test data slot names #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
diatomsRcool merged 1 commit into from
Oct 8, 2026
Merged

Update to clinical-microschemas v0.0.8 and fix test data slot names #4

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5,243 changes: 5,060 additions & 183 deletions docs/schema/bdc_variable_library.yaml
View file
Open in desktop

Large diffs are not rendered by default.

20,991 changes: 18,173 additions & 2,818 deletions src/bdc_variable_library/datamodel/bdc_variable_library.py
View file
Open in desktop

Large diffs are not rendered by default.

17,690 changes: 16,861 additions & 829 deletions src/bdc_variable_library/datamodel/bdc_variable_library_pydantic.py
View file
Open in desktop

Large diffs are not rendered by default.

14 changes: 9 additions & 5 deletions src/bdc_variable_library/schema/bdc_variable_library.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ default_range: string
imports:
- linkml:types
- https://raw.githubusercontent.com/linkml/linkml-microschema-profile/v0.3.0/src/linkml_microschema_profile/schema/linkml_microschema_profile
- https://raw.githubusercontent.com/linkml/clinical-microschemas/v0.0.5/src/clinical_microschemas/schema/clinical_microschemas
- https://raw.githubusercontent.com/linkml/clinical-microschemas/v0.0.8/src/clinical_microschemas/schema/clinical_microschemas

classes:

Expand Down Expand Up @@ -214,28 +214,28 @@ classes:
description: >-
Weight variable with metadata, measured in kg using a mechanical beam balance
instantiates:
- HumanBodyWeightRecord001
- AdultHumanBodyWeightRecord001

CompoundWeight002:
is_a: CompoundVariable
description: >-
Weight variable with metadata, measured in pounds using a mechanical beam balance
instantiates:
- HumanBodyWeightRecord002
- AdultHumanBodyWeightRecord002

CompoundWeight003:
is_a: CompoundVariable
description: >-
Weight variable with metadata, measured in kg using a body composition analyzer
instantiates:
- HumanBodyWeightRecord003
- AdultHumanBodyWeightRecord001

CompoundWeight004:
is_a: CompoundVariable
description: >-
Weight variable with metadata, measured in kg using a digital scale
instantiates:
- HumanBodyWeightRecord004
- AdultHumanBodyWeightRecord001

IntegratedWeight001:
is_a: IntegratedVariable
Expand Down Expand Up @@ -2198,4 +2198,8 @@ enums:
age_at_procedure_start:
age_at_procedure_end:
age_at_procedure_record:
procedure_status:
procedure_provenance:
exposure_status:
exposure_provenance:

2 changes: 1 addition & 1 deletion tests/data/valid/CompoundAspirin001-001test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ row_metadata:
- exposure_status
- id: CHSAGE01phv000987992s
microschema_slot:
- age_at_exposure_record
- age_at_drug_record
- id: CHSIndividual_IDphv00098771s
microschema_slot:
- subject_identifier
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundAspirin001-002test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ row_metadata:
- exposure_status
- id: HCHSSOLAGEphv00226251s
microschema_slot:
- age_at_exposure_record
- age_at_drug_record
- id: HCHSSOLSUBJECT_IDphv00226250s
microschema_slot:
- subject_identifier
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundAsthma001-001test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ bdchm_type: condition
documentation_metadata:
- contr_vocab: MONDO:0004979
microschema_slot:
- condition_concept
- condition_type
- contr_vocab: working_diagnosis
microschema_slot:
- condition_provenance
Expand Down
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundAsthma001-002test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ bdchm_type: condition
documentation_metadata:
- contr_vocab: MONDO:0004979
microschema_slot:
- condition_concept
- condition_type
- contr_vocab: oneself
microschema_slot:
- relationship_to_participant
Expand Down
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundHeartFailure001-002test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ bdchm_type: condition
documentation_metadata:
- contr_vocab: MONDO:0005009
microschema_slot:
- condition_concept
- condition_type
- contr_vocab: patient_self_report
microschema_slot:
- condition_provenance
Expand Down
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundHeartFailure001-test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ bdchm_type: condition
documentation_metadata:
- contr_vocab: MONDO:0005252
microschema_slot:
- condition_concept
- condition_type
- contr_vocab: health_record
microschema_slot:
- condition_provenance
Expand Down
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundHeight001-test.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,4 +22,4 @@ documentation_metadata:
- instrument
- contr_vocab: anthropometry
microschema_slot:
- method_type
- method
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundHeight002-test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ documentation_metadata:
- instrument
- contr_vocab: anthropometry
microschema_slot:
- method_type
- method
- contr_vocab: orthostatic_body_position
microschema_slot:
- body_position
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundObesity001-002test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ bdchm_type: condition
documentation_metadata:
- contr_vocab: MONDO:0005139
microschema_slot:
- condition_concept
- condition_type
- contr_vocab: working_diagnosis
microschema_slot:
- condition_provenance
Expand Down
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundObesity001-test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ bdchm_type: condition
documentation_metadata:
- contr_vocab: MONDO:0005139
microschema_slot:
- condition_concept
- condition_type
- contr_vocab: working_diagnosis
microschema_slot:
- condition_provenance
Expand Down
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundPacemaker001-001test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ documentation_metadata:
- procedure_provenance
- contr_vocab: UBERON:0000948
microschema_slot:
- affected_body_site
- body_location
row_metadata:
- id: ARICDSRA9phv00205047s
microschema_slot:
Expand Down
2 changes: 1 addition & 1 deletion tests/data/valid/CompoundPacemaker001-002test.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ documentation_metadata:
- procedure_provenance
- contr_vocab: UBERON:0000948
microschema_slot:
- affected_body_site
- body_location
row_metadata:
- id: WHIELE_PACEphv00155223s
microschema_slot:
Expand Down
Loading