Excluded rules summary (#24)

* Excluded rules summary

This adds a series of tables designed to help debug study configs
by providing a list of rules that were excluded, but were
considered potential candidates for exclusion.

This adds a new study arg, debug, which is used to enable these
tables. They are off by default.

* PR feedback

cumulus_library_opioid/manifest.toml

@@ -5,6 +5,7 @@ file_names = [
     "vocab/static_builder.py",
     "vocab/rxnorm_vsac_builder.py",
     "vocab/additional_rules_builder.py",
+    "vocab/excluded_rules_builder.py",
 ]
 
 # [sql_config]

cumulus_library_opioid/reference_sql/excluded_rules_builder.sql

@@ -0,0 +1,130 @@
+-- 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__acep_excluded_rules AS 
+SELECT 
+    rxcui1,
+    rxcui2,
+    tty1,
+    tty2,
+    rui,
+    rel,
+    rela,
+    str1,
+    str2,
+    keyword
+FROM
+    opioid__acep_potential_rules
+WHERE rui NOT IN (SELECT DISTINCT rui from opioid__acep_combined_ruleset)
+AND rxcui1 NOT IN (SELECT DISTINCT rxcui1 from opioid__acep_combined_ruleset)   
+AND rxcui2 NOT IN (SELECT DISTINCT rxcui2 from opioid__acep_combined_ruleset)
+
+-- ###########################################################
+
+CREATE VIEW opioid__acep_excluded_tradename AS 
+SELECT 
+    rxcui1,
+    tty1,
+    rel,
+    rela,
+    rxcui2,
+    tty2,
+    str2
+FROM
+    opioid__acep_excluded_rules
+WHERE rela IN ('has_tradename','tradename_of')
+
+-- ###########################################################
+
+CREATE VIEW opioid__acep_excluded_consists AS 
+SELECT 
+    rxcui1,
+    tty1,
+    rel,
+    rela,
+    rxcui2,
+    tty2,
+    str2
+FROM
+    opioid__acep_excluded_rules
+WHERE rela IN ('consists_of','constitutes')
+
+-- ###########################################################
+
+CREATE VIEW opioid__acep_excluded_is_a AS 
+SELECT 
+    rxcui1,
+    tty1,
+    rel,
+    rela,
+    rxcui2,
+    tty2,
+    str2
+FROM
+    opioid__acep_excluded_rules
+WHERE rela IN ('isa','inverse_isa')
+
+-- ###########################################################
+
+CREATE VIEW opioid__acep_excluded_ingredient AS 
+SELECT 
+    rxcui1,
+    tty1,
+    rel,
+    rela,
+    rxcui2,
+    tty2,
+    str2
+FROM
+    opioid__acep_excluded_rules
+WHERE rela IN ('has_ingredient','ingredient_of','has_precise_ingredient','precise_ingredient_of','has_ingredients','ingredients_of')
+
+-- ###########################################################
+
+CREATE VIEW opioid__acep_excluded_dose_form AS 
+SELECT 
+    rxcui1,
+    tty1,
+    rel,
+    rela,
+    rxcui2,
+    tty2,
+    str2
+FROM
+    opioid__acep_excluded_rules
+WHERE rela IN ('dose_form_of','has_dose_form','doseformgroup_of','has_doseformgroup')
+
+-- ###########################################################
+
+CREATE VIEW opioid__acep_excluded_form AS 
+SELECT 
+    rxcui1,
+    tty1,
+    rel,
+    rela,
+    rxcui2,
+    tty2,
+    str2
+FROM
+    opioid__acep_excluded_rules
+WHERE rela IN ('form_of','has_form')
+
+-- ###########################################################
+
+CREATE VIEW opioid__acep_excluded_other AS 
+SELECT 
+    rxcui1,
+    tty1,
+    rel,
+    rela,
+    rxcui2,
+    tty2,
+    str2
+FROM
+    opioid__acep_excluded_rules
+WHERE rela NOT IN ('has_tradename','tradename_of','consists_of','constitutes','isa','inverse_isa','has_ingredient','ingredient_of','has_precise_ingredient','precise_ingredient_of','has_ingredients','ingredients_of','dose_form_of','has_dose_form','doseformgroup_of','has_doseformgroup','form_of','has_form')