Merge pull request #20 from smart-on-fhir/mg/additional_rules

Additional rules search

cumulus_library_opioid/manifest.toml

@@ -4,6 +4,7 @@ study_prefix = "opioid"
 file_names = [
     "vocab/static_builder.py",
     "vocab/rxnorm_vsac_builder.py",
+    "vocab/additional_rules_builder.py",
 ]
 
 [sql_config]

cumulus_library_opioid/reference_sql/additional_rules_builder.sql

@@ -0,0 +1,116 @@
+-- noqa: disable=all
+-- This sql was autogenerated as a reference example using the library
+-- CLI. Its format is tied to the specific database it was run against,
+-- and it may not be correct for all databases. Use the CLI's build 
+-- option to derive the best SQL for your dataset.
+
+-- ###########################################################
+
+CREATE TABLE opioid__search_rules_descriptions AS 
+    SELECT 
+        e.tty1,
+        e.rela,
+        e.tty2,
+        e.rule,
+        e.include,
+        u1.tty_str AS tty1_str,
+        u2.tty_str AS tty2_str
+    FROM
+        opioid__umls_tty as u1,
+        opioid__umls_tty as u2,
+        opioid__search_rules as e
+    WHERE
+        u1.tty = e.tty1
+        AND u2.tty = e.tty2
+
+-- ###########################################################
+
+CREATE OR REPLACE VIEW opioid__acep_potential_rules AS
+SELECT
+    s.rxcui AS rxcui1,
+    r.rxcui AS rxcui2,
+    s.tty AS tty1,
+    r.tty AS tty2,
+    s.rui,
+    s.rel,
+    s.rela,
+    s.str AS str1,
+    r.str AS str2,
+    r.keyword
+FROM opioid__all_rxnconso_keywords AS r,
+    opioid__acep_rela AS s
+WHERE
+    s.rxcui2 = r.rxcui
+    AND s.rxcui2 NOT IN (SELECT DISTINCT RXCUI FROM opioid__acep_rxnconso_keywords)
+
+-- ###########################################################
+
+CREATE OR REPLACE VIEW opioid__acep_included_rels AS
+SELECT
+    r.rxcui1,
+    r.rxcui2,
+    r.tty1,
+    r.tty2,
+    r.rui,
+    r.rel,
+    r.rela,
+    r.str1,
+    r.str2,
+    r.keyword
+FROM opioid__acep_potential_rules AS r,
+    opioid__search_rules AS e
+WHERE
+    r.REL NOT IN ('RB', 'PAR')
+    AND e.include = TRUE
+    AND r.TTY1 = e.TTY1
+    AND r.TTY2 = e.TTY2
+    AND r.RELA = e.RELA
+
+-- ###########################################################
+
+CREATE OR REPLACE VIEW opioid__acep_included_keywords AS
+SELECT
+    r.rxcui1,
+    r.rxcui2,
+    r.tty1,
+    r.tty2,
+    r.rui,
+    r.rel,
+    r.rela,
+    r.str1,
+    r.str2,
+    r.keyword
+FROM opioid__acep_potential_rules AS r
+WHERE
+    r.REL NOT IN ('RB', 'PAR')
+    AND length(r.keyword) >= 4
+
+-- ###########################################################
+
+CREATE TABLE opioid__acep_combined_ruleset AS
+SELECT
+rxcui1,
+rxcui2,
+tty1,
+tty2,
+rui,
+rel,
+rela,
+str1,
+str2,
+keyword
+FROM opioid__acep_included_keywords
+UNION
+SELECT
+rxcui1,
+rxcui2,
+tty1,
+tty2,
+rui,
+rel,
+rela,
+str1,
+str2,
+keyword
+FROM opioid__acep_included_rels
+

cumulus_library_opioid/reference_sql/rxnorm_vsac_builder.sql

@@ -0,0 +1,88 @@
+-- noqa: disable=all
+-- This sql was autogenerated as a reference example using the library
+-- CLI. Its format is tied to the specific database it was run against,
+-- and it may not be correct for all databases. Use the CLI's build 
+-- option to derive the best SQL for your dataset.
+
+-- ###########################################################
+
+CREATE OR REPLACE VIEW opioid__acep_rxnconso AS
+SELECT
+    a.rxcui,
+    a.str,
+    a.tty,
+    a.sab,
+    a.code
+FROM rxnorm.rxnconso AS a,
+    opioid__acep_vsac AS b
+WHERE
+    a.rxcui = b.code
+
+-- ###########################################################
+
+CREATE OR REPLACE VIEW opioid__acep_rxnconso_keywords AS
+SELECT
+    a.rxcui,
+    a.str,
+    a.tty,
+    a.sab,
+    a.code,
+    b.str AS keyword
+FROM opioid__acep_rxnconso AS a,
+    opioid__keywords AS b
+WHERE
+    lower(a.str) LIKE concat('%',b.STR, '%')
+
+-- ###########################################################
+
+CREATE OR REPLACE VIEW opioid__acep_rxnsty AS
+SELECT
+    a.rxcui,
+    a.tui,
+    a.stn,
+    a.sty,
+    a.atui,
+    a.cvf
+FROM rxnorm.rxnsty AS a,
+    opioid__acep_vsac AS b
+WHERE
+    a.rxcui = b.code
+
+-- ###########################################################
+
+CREATE OR REPLACE VIEW opioid__acep_rxnrel AS
+SELECT
+    a.rxcui1,
+    a.rxaui1,
+    a.stype1,
+    a.rel,
+    a.rxcui2,
+    a.rxaui2,
+    a.stype2,
+    a.rela,
+    a.rui,
+    a.srui,
+    a.sab,
+    a.sl,
+    a.rg
+FROM rxnorm.rxnrel AS a,
+    opioid__acep_vsac AS b
+WHERE
+    a.rxcui1 = b.code
+
+-- ###########################################################
+
+CREATE OR REPLACE VIEW opioid__acep_rela AS
+SELECT
+    a.rxcui,
+    a.str,
+    a.tty,
+    a.sab,
+    b.rxcui2,
+    b.rel,
+    b.rela,
+    b.rui
+FROM opioid__acep_rxnconso_keywords AS a,
+    opioid__acep_RXNREL AS b
+WHERE
+    a.rxcui = b.rxcui1

cumulus_library_opioid/reference_sql/static_builder.sql

@@ -0,0 +1,62 @@
+-- noqa: disable=all
+-- This sql was autogenerated as a reference example using the library
+-- CLI. Its format is tied to the specific database it was run against,
+-- and it may not be correct for all databases. Use the CLI's build 
+-- option to derive the best SQL for your dataset.
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `cumulus_mhg_dev_db`.`opioid__keywords` (
+    STR STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucketname/path_to_db_storage/opioid/keywords.filtered'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `cumulus_mhg_dev_db`.`opioid__all_rxnconso_keywords` (
+    RXCUI STRING,
+    STR STRING,
+    TTY STRING,
+    SAB STRING,
+    CODE STRING,
+    keyword STRING,
+    keyword_len STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucketname/path_to_db_storage/opioid/all_rxcui_str.RXNCONSO_curated'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `cumulus_mhg_dev_db`.`opioid__search_rules` (
+    TTY1 STRING,
+    RELA STRING,
+    TTY2 STRING,
+    rule STRING,
+    include BOOLEAN
+)
+STORED AS PARQUET
+LOCATION 's3://bucketname/path_to_db_storage/opioid/expand_rules'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `cumulus_mhg_dev_db`.`opioid__umls_tty` (
+    TTY STRING,
+    TTY_STR STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucketname/path_to_db_storage/opioid/umls_tty'
+tblproperties ("parquet.compression"="SNAPPY");
+
+-- ###########################################################
+
+CREATE EXTERNAL TABLE IF NOT EXISTS `cumulus_mhg_dev_db`.`opioid__acep_vsac` (
+    code STRING,
+    display STRING
+)
+STORED AS PARQUET
+LOCATION 's3://bucketname/path_to_db_storage/opioid/acep'
+tblproperties ("parquet.compression"="SNAPPY");