Replaced wildcard match with regex

cumulus_library/databases.py

@@ -13,6 +13,7 @@
 import json
 import os
 import pathlib
+import re
 import sys
 from pathlib import Path
 from typing import Any, Protocol
@@ -341,6 +342,13 @@ def __init__(self, db_file: str):
             None,
             duckdb.typing.VARCHAR,
         )
+        self.connection.create_function(
+            # DuckDB's version is regexp_matches.
+            "regexp_like",
+            self._compat_regexp_like,
+            None,
+            duckdb.typing.BOOLEAN,
+        )
         self.connection.create_function(
             # We frequently use Athena's date() function because it's easier than
             # the more widely-supported way of CAST(x AS DATE).
@@ -393,6 +401,13 @@ def _compat_array_join(
             return None
         return delimiter.join(v for v in value if v is not None)
 
+    @staticmethod
+    def _compat_regexp_like(string: str | None, pattern: str | None) -> bool:
+        if string is None or pattern is None:
+            return None
+        match = re.search(pattern, string)
+        return match is not None
+
     @staticmethod
     def _compat_date(
         value: str | datetime.datetime | datetime.date | None,

cumulus_library/studies/core/core_templates/medication.sql.jinja

@@ -1,4 +1,5 @@
 {% import 'core_utils.jinja' as utils -%}
+{% import 'syntax.sql.jinja' as syntax -%}
 
 CREATE TABLE core__medication AS (
     WITH
@@ -32,15 +33,15 @@ CREATE TABLE core__medication AS (
             mr.id,
             substring(mr.med_ref, 2) AS medication_id
         FROM mr_basics AS mr
-        WHERE mr.med_ref IS NOT NULL AND mr.med_ref LIKE '#%'
+        WHERE mr.med_ref IS NOT NULL AND {{ syntax.like('mr.med_ref', '#%') }}
     ),
 
     external_refs AS (
         SELECT DISTINCT
             mr.id,
             substring(mr.med_ref, 12) AS medication_id
         FROM mr_basics AS mr
-        WHERE mr.med_ref IS NOT NULL AND mr.med_ref LIKE 'Medication/%'
+        WHERE mr.med_ref IS NOT NULL AND {{ syntax.like('mr.med_ref', 'Medication/%') }}
     )
 
     {# Internal: medication data from inline ETL extraction.

cumulus_library/studies/core/reference_sql/builder_condition.sql

@@ -72,7 +72,7 @@ CREATE TABLE core__condition_dn_clinical_status AS (
             condition AS s,
             UNNEST(s.clinicalStatus.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://terminology.hl7.org/CodeSystem/condition-clinical'
+            REGEXP_LIKE(u.coding.system, 'http://terminology\.hl7\.org/CodeSystem/condition-clinical')
     ), --noqa: LT07
 
     union_table AS (
@@ -137,7 +137,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             condition AS s,
             UNNEST(s.code.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://snomed.info/sct'
+            REGEXP_LIKE(u.coding.system, 'http://snomed\.info/sct')
     ), --noqa: LT07
 
     system_code_1 AS (
@@ -153,7 +153,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             condition AS s,
             UNNEST(s.code.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://hl7.org/fhir/sid/icd-10-cm'
+            REGEXP_LIKE(u.coding.system, 'http://hl7\.org/fhir/sid/icd-10-cm')
     ), --noqa: LT07
 
     system_code_2 AS (
@@ -169,7 +169,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             condition AS s,
             UNNEST(s.code.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://hl7.org/fhir/sid/icd-9-cm'
+            REGEXP_LIKE(u.coding.system, 'http://hl7\.org/fhir/sid/icd-9-cm')
     ), --noqa: LT07
 
     system_code_3 AS (
@@ -185,7 +185,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             condition AS s,
             UNNEST(s.code.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://hl7.org/fhir/sid/icd-9-cm/diagnosis'
+            REGEXP_LIKE(u.coding.system, 'http://hl7\.org/fhir/sid/icd-9-cm/diagnosis')
     ), --noqa: LT07
 
     system_code_4 AS (
@@ -201,7 +201,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             condition AS s,
             UNNEST(s.code.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'urn:oid:1.2.840.114350.1.13.71.2.7.2.728286'
+            REGEXP_LIKE(u.coding.system, 'urn:oid:1\.2\.840\.114350\.1\.13\.71\.2\.7\.2\.728286')
     ), --noqa: LT07
 
     system_code_5 AS (
@@ -217,7 +217,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             condition AS s,
             UNNEST(s.code.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'urn:oid:1.2.840.114350.1.13.71.2.7.4.698084.10375'
+            REGEXP_LIKE(u.coding.system, 'urn:oid:1\.2\.840\.114350\.1\.13\.71\.2\.7\.4\.698084\.10375')
     ), --noqa: LT07
 
     system_code_6 AS (
@@ -233,7 +233,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             condition AS s,
             UNNEST(s.code.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://terminology.hl7.org/CodeSystem/data-absent-reason'
+            REGEXP_LIKE(u.coding.system, 'http://terminology\.hl7\.org/CodeSystem/data-absent-reason')
     ), --noqa: LT07
 
     union_table AS (
@@ -397,7 +397,7 @@ CREATE TABLE core__condition_dn_verification_status AS (
             condition AS s,
             UNNEST(s.verificationStatus.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://terminology.hl7.org/CodeSystem/condition-ver-status'
+            REGEXP_LIKE(u.coding.system, 'http://terminology\.hl7\.org/CodeSystem/condition-ver-status')
     ), --noqa: LT07
 
     union_table AS (

cumulus_library/studies/core/reference_sql/builder_documentreference.sql

@@ -71,7 +71,7 @@ CREATE TABLE core__documentreference_dn_category AS (
             flattened_rows AS s,
             UNNEST(s.category.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://hl7.org/fhir/us/core/ValueSet/us-core-documentreference-category'
+            REGEXP_LIKE(u.coding.system, 'http://hl7\.org/fhir/us/core/ValueSet/us-core-documentreference-category')
     ), --noqa: LT07
 
     union_table AS (

cumulus_library/studies/core/reference_sql/builder_encounter.sql

@@ -32,7 +32,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://terminology.hl7.org/CodeSystem/encounter-type'
+            REGEXP_LIKE(u.coding.system, 'http://terminology\.hl7\.org/CodeSystem/encounter-type')
     ), --noqa: LT07
 
     system_type_1 AS (
@@ -48,7 +48,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://terminology.hl7.org/CodeSystem/v2-0004'
+            REGEXP_LIKE(u.coding.system, 'http://terminology\.hl7\.org/CodeSystem/v2-0004')
     ), --noqa: LT07
 
     system_type_2 AS (
@@ -64,7 +64,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'urn:oid:2.16.840.1.113883.4.642.3.248'
+            REGEXP_LIKE(u.coding.system, 'urn:oid:2\.16\.840\.1\.113883\.4\.642\.3\.248')
     ), --noqa: LT07
 
     system_type_3 AS (
@@ -80,7 +80,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://snomed.info/sct'
+            REGEXP_LIKE(u.coding.system, 'http://snomed\.info/sct')
     ), --noqa: LT07
 
     system_type_4 AS (
@@ -96,7 +96,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'https://fhir.cerner.com/%/codeSet/71'
+            REGEXP_LIKE(u.coding.system, 'https://fhir\.cerner\.com/.*/codeSet/71')
     ), --noqa: LT07
 
     system_type_5 AS (
@@ -112,7 +112,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'urn:oid:1.2.840.114350.1.13.71.2.7.10.698084.10110'
+            REGEXP_LIKE(u.coding.system, 'urn:oid:1\.2\.840\.114350\.1\.13\.71\.2\.7\.10\.698084\.10110')
     ), --noqa: LT07
 
     system_type_6 AS (
@@ -128,7 +128,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'urn:oid:1.2.840.114350.1.13.71.2.7.10.698084.18875'
+            REGEXP_LIKE(u.coding.system, 'urn:oid:1\.2\.840\.114350\.1\.13\.71\.2\.7\.10\.698084\.18875')
     ), --noqa: LT07
 
     system_type_7 AS (
@@ -144,7 +144,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'urn:oid:1.2.840.114350.1.13.71.2.7.10.698084.30'
+            REGEXP_LIKE(u.coding.system, 'urn:oid:1\.2\.840\.114350\.1\.13\.71\.2\.7\.10\.698084\.30')
     ), --noqa: LT07
 
     system_type_8 AS (
@@ -160,7 +160,7 @@ CREATE TABLE core__encounter_dn_type AS (
             flattened_rows AS s,
             UNNEST(s.type.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'urn:oid:1.2.840.114350.1.13.71.2.7.2.808267'
+            REGEXP_LIKE(u.coding.system, 'urn:oid:1\.2\.840\.114350\.1\.13\.71\.2\.7\.2\.808267')
     ), --noqa: LT07
 
     union_table AS (
@@ -340,7 +340,7 @@ CREATE TABLE core__encounter_dn_reasoncode AS (
             flattened_rows AS s,
             UNNEST(s.reasoncode.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://terminology.hl7.org/CodeSystem/v3-ActPriority'
+            REGEXP_LIKE(u.coding.system, 'http://terminology\.hl7\.org/CodeSystem/v3-ActPriority')
     ), --noqa: LT07
 
     system_reasoncode_1 AS (
@@ -356,7 +356,7 @@ CREATE TABLE core__encounter_dn_reasoncode AS (
             flattened_rows AS s,
             UNNEST(s.reasoncode.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://snomed.info/sct'
+            REGEXP_LIKE(u.coding.system, 'http://snomed\.info/sct')
     ), --noqa: LT07
 
     system_reasoncode_2 AS (
@@ -372,7 +372,7 @@ CREATE TABLE core__encounter_dn_reasoncode AS (
             flattened_rows AS s,
             UNNEST(s.reasoncode.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://hl7.org/fhir/sid/icd-10-cm'
+            REGEXP_LIKE(u.coding.system, 'http://hl7\.org/fhir/sid/icd-10-cm')
     ), --noqa: LT07
 
     system_reasoncode_3 AS (
@@ -388,7 +388,7 @@ CREATE TABLE core__encounter_dn_reasoncode AS (
             flattened_rows AS s,
             UNNEST(s.reasoncode.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'http://hl7.org/fhir/sid/icd-9-cm'
+            REGEXP_LIKE(u.coding.system, 'http://hl7\.org/fhir/sid/icd-9-cm')
     ), --noqa: LT07
 
     system_reasoncode_4 AS (
@@ -404,7 +404,7 @@ CREATE TABLE core__encounter_dn_reasoncode AS (
             flattened_rows AS s,
             UNNEST(s.reasoncode.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'https://fhir.cerner.com/%/nomenclature'
+            REGEXP_LIKE(u.coding.system, 'https://fhir\.cerner\.com/.*/nomenclature')
     ), --noqa: LT07
 
     system_reasoncode_5 AS (
@@ -420,7 +420,7 @@ CREATE TABLE core__encounter_dn_reasoncode AS (
             flattened_rows AS s,
             UNNEST(s.reasoncode.coding) AS u (coding)
         WHERE
-            u.coding.system LIKE 'urn:oid:1.2.840.114350.1.13.71.2.7.2.728286'
+            REGEXP_LIKE(u.coding.system, 'urn:oid:1\.2\.840\.114350\.1\.13\.71\.2\.7\.2\.728286')
     ), --noqa: LT07
 
     union_table AS (

cumulus_library/studies/core/reference_sql/builder_medication.sql

@@ -86,15 +86,17 @@ CREATE TABLE core__medication AS (
             mr.id,
             substring(mr.med_ref, 2) AS medication_id
         FROM mr_basics AS mr
-        WHERE mr.med_ref IS NOT NULL AND mr.med_ref LIKE '#%'
+        WHERE mr.med_ref IS NOT NULL AND REGEXP_LIKE(mr.med_ref, '#.*')
+        )
     ),
 
     external_refs AS (
         SELECT DISTINCT
             mr.id,
             substring(mr.med_ref, 12) AS medication_id
         FROM mr_basics AS mr
-        WHERE mr.med_ref IS NOT NULL AND mr.med_ref LIKE 'Medication/%'
+        WHERE mr.med_ref IS NOT NULL AND REGEXP_LIKE(mr.med_ref, 'Medication/.*')
+        )
     )
 
 

cumulus_library/template_sql/codeable_concept_denormalize.sql.jinja

@@ -79,7 +79,7 @@ CREATE TABLE {{ target_table }} AS (
             UNNEST(s.{{ field_alias }}.coding) AS u (coding)
         {%- if filter_priority %}
         WHERE
-            u.coding.system LIKE '{{ system }}'
+            {{ syntax.like('u.coding.system', system) }}
         {%- endif %}
     ), --noqa: LT07
     {%- endfor %}

cumulus_library/template_sql/coding_denormalize.sql.jinja

@@ -17,7 +17,7 @@ CREATE TABLE {{ target_table }} AS (
             UNNEST(s.{{ parent_field }}) AS u (parent_col)
         {%- if filter_priority %}
         WHERE
-            u.parent_col.{{ column_name }}.system LIKE '{{ system }}'
+            {{ syntax.like("u.parent_col." + column_name + ".system", system) }}
         {%- endif %}
     ), --noqa: LT07
     {%- endfor %}

cumulus_library/template_sql/shared_macros/syntax.sql.jinja

@@ -1,4 +1,4 @@
-{# Commonly used macros related to basic SQL syntax formatting #}
+{# Commonly used macros related to basic SQL syntax formatting #}-- noqa:disable=JJ01
 
 {%- macro comma_delineate(loop) -%}
 {%- if not loop.last -%}
@@ -17,4 +17,32 @@
 UNION
 {%- endif -%}
 {%- endmacro -%}
+
+{#- The intent of this macro is to convert sql wildcard format to regex syntax.
+ So for example, a value of macro_string like:
+
+https://fhir.cerner.com/%/codeSet/71
+
+will be converted into a regex-escaped pattern with a regex match anything pattern:
+
+https:\/\/fhir\.cerner\.com\/(.*)\/codeSet\/71 
+
+See https://trino.io/docs/current/functions/regexp.html for more information. We
+are applying a limited ruleset currently, since this is based on common patterns
+in coding system fields, where this is currently used; if needed this could be
+made more robust.
+-#}
+{%- macro wildcard_to_regex(match_string) -%}
+'^{{ match_string.replace("\'", "\\\''").replace(".", "\\.").replace("%", ".*") }}$'
+{%- endmacro -%}
+
+
+{#- This macro provides a SQL LIKE-esque interface to abstract away having to
+worry about the slightly more performant regex based matching we want to use
+in most cases.
+-#}
+{%- macro like(field, match_string) -%}
+REGEXP_LIKE({{ field }}, {{ wildcard_to_regex(match_string) }})
+{%- endmacro -%}
+
 --noqa: LT12

cumulus_library/template_sql/show_tables.sql.jinja

@@ -1,6 +1,7 @@
+{%- import 'syntax.sql.jinja' as syntax -%}
 SELECT table_name
 FROM information_schema.tables
 WHERE
     table_schema = '{{ schema_name }}'
     AND table_type = 'BASE TABLE'
-    AND table_name LIKE '{{ prefix }}%';
+    AND {{ syntax.like('table_name', prefix +"%") }}

cumulus_library/template_sql/show_views.sql.jinja

@@ -1,6 +1,7 @@
+{%- import 'syntax.sql.jinja' as syntax -%}
 SELECT table_name
 FROM information_schema.tables
 WHERE
     table_schema = '{{ schema_name }}'
     AND table_type = 'VIEW'
-    AND table_name LIKE '{{ prefix }}%';
+    AND {{ syntax.like('table_name', prefix + "%") }}