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Add AllergyIntolerance support to core study
- Adds core__allergyintolerance - Adds core__count_allergyintolerance_month
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66 changes: 66 additions & 0 deletions
66
cumulus_library/studies/core/builder_allergyintolerance.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| import cumulus_library | ||
| from cumulus_library.studies.core.core_templates import core_templates | ||
| from cumulus_library.template_sql import sql_utils | ||
|
|
||
| expected_table_cols = { | ||
| "allergyintolerance": { | ||
| "id": [], | ||
| "type": [], | ||
| "category": [], | ||
| "criticality": [], | ||
| "recordedDate": [], | ||
| "patient": sql_utils.REFERENCE, | ||
| "encounter": sql_utils.REFERENCE, | ||
| "reaction": ["severity"], | ||
| } | ||
| } | ||
|
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|
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| class CoreAllergyIntoleranceBuilder(cumulus_library.BaseTableBuilder): | ||
| display_text = "Creating AllergyIntolerance tables..." | ||
|
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| def prepare_queries(self, *args, config: cumulus_library.StudyConfig, **kwargs): | ||
| code_sources = [ | ||
| sql_utils.CodeableConceptConfig( | ||
| source_table="allergyintolerance", | ||
| column_hierarchy=[("clinicalStatus", dict)], | ||
| target_table="core__allergyintolerance_dn_clinical_status", | ||
| filter_priority=True, | ||
| code_systems=[ | ||
| # Restrict to just this required binding system | ||
| "http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical", | ||
| ], | ||
| ), | ||
| sql_utils.CodeableConceptConfig( | ||
| source_table="allergyintolerance", | ||
| column_hierarchy=[("verificationStatus", dict)], | ||
| target_table="core__allergyintolerance_dn_verification_status", | ||
| filter_priority=True, | ||
| code_systems=[ | ||
| # Restrict to just this required binding system | ||
| "http://terminology.hl7.org/CodeSystem/allergyintolerance-verification", | ||
| ], | ||
| ), | ||
| sql_utils.CodeableConceptConfig( | ||
| source_table="allergyintolerance", | ||
| column_hierarchy=[("code", dict)], | ||
| target_table="core__allergyintolerance_dn_code", | ||
| ), | ||
| sql_utils.CodeableConceptConfig( | ||
| source_table="allergyintolerance", | ||
| column_hierarchy=[("reaction", list), ("substance", dict)], | ||
| target_table="core__allergyintolerance_dn_reaction_substance", | ||
| expected={"substance": sql_utils.CODEABLE_CONCEPT}, | ||
| ), | ||
| sql_utils.CodeableConceptConfig( | ||
| source_table="allergyintolerance", | ||
| column_hierarchy=[("reaction", list), ("manifestation", list)], | ||
| target_table="core__allergyintolerance_dn_reaction_manifestation", | ||
| expected={"manifestation": sql_utils.CODEABLE_CONCEPT}, | ||
| ), | ||
| ] | ||
| self.queries += sql_utils.denormalize_complex_objects(config.db, code_sources) | ||
| validated_schema = sql_utils.validate_schema(config.db, expected_table_cols) | ||
| self.queries.append( | ||
| core_templates.get_core_template("allergyintolerance", validated_schema) | ||
| ) |
138 changes: 138 additions & 0 deletions
138
cumulus_library/studies/core/core_templates/allergyintolerance.sql.jinja
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| {% import 'core_utils.jinja' as utils %} | ||
| {% import 'unnest_utils.jinja' as unnest_utils %} | ||
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| CREATE TABLE core__allergyintolerance AS | ||
| WITH temp_allergyintolerance AS ( | ||
| SELECT | ||
| {{- | ||
| utils.basic_cols( | ||
| 'allergyintolerance', | ||
| 'a', | ||
| [ | ||
| 'id', | ||
| ] | ||
| ) | ||
| }}, | ||
| {{- | ||
| utils.nullable_cols( | ||
| 'allergyintolerance', | ||
| 'a', | ||
| [ | ||
| 'type', | ||
| 'category', | ||
| 'criticality', | ||
| ('patient', 'reference', 'patient_ref'), | ||
| ('encounter', 'reference', 'encounter_ref'), | ||
| ], | ||
| schema | ||
| ) | ||
| }}, | ||
| {{- | ||
| utils.date_cols_from_str( | ||
| 'allergyintolerance', | ||
| 'a', | ||
| ['recordedDate'], | ||
| schema | ||
| ) | ||
| }}, | ||
| {{- | ||
| utils.truncate_date_cols( | ||
| 'allergyintolerance', | ||
| 'a', | ||
| [ | ||
| ('recordedDate', 'week'), | ||
| ('recordedDate', 'month'), | ||
| ('recordedDate', 'year'), | ||
| ], | ||
| schema | ||
| ) | ||
| }} | ||
| FROM allergyintolerance AS a | ||
| ), | ||
|
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||
| temp_category AS ( | ||
| SELECT | ||
| a.id, | ||
| t.category | ||
| FROM | ||
| allergyintolerance AS a, | ||
| UNNEST(a.category) AS t (category) | ||
| ), | ||
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| flattened_reaction AS ({{ unnest_utils.flatten('allergyintolerance', 'reaction') }}), | ||
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| temp_reaction AS ( | ||
| SELECT | ||
| r.id, | ||
| r.row, | ||
| dn_subs.code AS substance_code, | ||
| dn_subs.system AS substance_system, | ||
| dn_subs.display AS substance_display, | ||
| dn_man.code AS manifestation_code, | ||
| dn_man.system AS manifestation_system, | ||
| dn_man.display AS manifestation_display, | ||
| {{- | ||
| utils.nullable_cols( | ||
| 'allergyintolerance', | ||
| 'r', | ||
| [ | ||
| ('reaction', 'severity', 'severity'), | ||
| ], | ||
| schema | ||
| ) | ||
| }} | ||
| FROM flattened_reaction AS r | ||
| LEFT JOIN core__allergyintolerance_dn_reaction_substance AS dn_subs | ||
| ON r.id = dn_subs.id AND r.row = dn_subs.row | ||
| LEFT JOIN core__allergyintolerance_dn_reaction_manifestation AS dn_man | ||
| ON r.id = dn_man.id AND r.row = dn_man.row | ||
| ) | ||
|
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||
| SELECT | ||
| ta.id, | ||
| CONCAT('AllergyIntolerance/', ta.id) AS allergyintolerance_ref, | ||
|
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| {#- We don't expose system for these next two since we filter | ||
| down to a single system in the denormalization table #} | ||
| dn_cstat.code AS clinicalStatus_code, | ||
| dn_vstat.code AS verificationStatus_code, | ||
|
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||
| {#- type, category, and criticality are not in US Core. | ||
| But they are useful for clinical interpretation. #} | ||
| ta.type, | ||
| tcat.category, | ||
| ta.criticality, | ||
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| dn_code.code AS code_code, | ||
| dn_code.system AS code_system, | ||
| dn_code.display AS code_display, | ||
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| ta.patient_ref, | ||
| ta.encounter_ref, | ||
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| {#- recordedDate is not in US Core. | ||
| But it's useful for looking at only a study period of data. #} | ||
| ta.recordedDate, | ||
| ta.recordedDate_week, | ||
| ta.recordedDate_month, | ||
| ta.recordedDate_year, | ||
|
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||
| {#- reaction.substance and reaction.severity are not in US Core. | ||
| But they are useful for clinical interpretation. #} | ||
| tr.row AS reaction_row, | ||
| tr.substance_code AS reaction_substance_code, | ||
| tr.substance_system AS reaction_substance_system, | ||
| tr.substance_display AS reaction_substance_display, | ||
| tr.manifestation_code AS reaction_manifestation_code, | ||
| tr.manifestation_system AS reaction_manifestation_system, | ||
| tr.manifestation_display AS reaction_manifestation_display, | ||
| tr.severity AS reaction_severity | ||
|
|
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| FROM temp_allergyintolerance AS ta | ||
| LEFT JOIN temp_reaction AS tr ON ta.id = tr.id | ||
| LEFT JOIN core__allergyintolerance_dn_code AS dn_code ON ta.id = dn_code.id | ||
| LEFT JOIN core__allergyintolerance_dn_clinical_status AS dn_cstat ON ta.id = dn_cstat.id | ||
| LEFT JOIN core__allergyintolerance_dn_verification_status AS dn_vstat | ||
| ON ta.id = dn_vstat.id | ||
| LEFT JOIN temp_category AS tcat ON ta.id = tcat.id | ||
| WHERE ta.recordedDate BETWEEN DATE('2016-01-01') AND CURRENT_DATE; |
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