Deprecate observation notice, optional fields, sql writing guide (#280)

* optional fields/deprecation docs

* Added sql guide

* sql regen

* PR feedback

* table doc update

.github/pull_request_template.md

@@ -1,5 +1,5 @@
 
 ### Checklist
-- [ ] Consider if documentation (like in `docs/`) needs to be updated
+- [ ] Consider if documentation (like in `docs/`, or if you've changed the structure of a table) needs to be updated
 - [ ] Consider if tests should be added
 - [ ] Update template repo if there are changes to study configuration

cumulus_library/studies/core/reference_sql/builder_condition.sql

@@ -25,7 +25,7 @@ CREATE TABLE core__condition_dn_category AS (
             s.row,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             flattened_rows AS s,
@@ -66,7 +66,7 @@ CREATE TABLE core__condition_dn_clinical_status AS (
             '0' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -131,7 +131,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             '0' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -147,7 +147,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             '1' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -163,7 +163,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             '2' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -179,7 +179,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             '3' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -195,7 +195,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             '4' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -211,7 +211,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             '5' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -227,7 +227,7 @@ CREATE TABLE core__condition_codable_concepts_display AS (
             '6' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -351,7 +351,7 @@ CREATE TABLE core__condition_codable_concepts_all AS (
             0 AS row,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,
@@ -391,7 +391,7 @@ CREATE TABLE core__condition_dn_verification_status AS (
             '0' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             condition AS s,

cumulus_library/studies/core/reference_sql/builder_documentreference.sql

@@ -15,7 +15,7 @@ CREATE TABLE core__documentreference_dn_type AS (
             0 AS row,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             documentreference AS s,
@@ -65,7 +65,7 @@ CREATE TABLE core__documentreference_dn_category AS (
             '0' AS priority,
             u.coding.code,
             u.coding.display,
-            u.coding.system AS system,
+            u.coding.system,
             u.coding.userSelected
         FROM
             flattened_rows AS s,
@@ -121,38 +121,16 @@ CREATE TABLE core__documentreference_dn_category AS (
 
 -- ###########################################################
 
-CREATE TABLE core__documentreference_dn_format AS (
-    WITH
-
-    system_format_0 AS (
-        SELECT DISTINCT
-            s.id AS id,
-            u.parent_col.format.code,
-            u.parent_col.format.display,
-            u.parent_col.format.system AS system
-        FROM
-            documentreference AS s,
-            UNNEST(s.content) AS u (parent_col)
-    ), --noqa: LT07
-
-    union_table AS (
-        SELECT
-            id,
-            system,
-            code,
-            display
-        FROM system_format_0
-
+CREATE TABLE IF NOT EXISTS "cumulus_mhg_dev_db"."core__documentreference_dn_format"
+AS (
+    SELECT * FROM (
+        VALUES
+        (cast(NULL AS varchar),cast(NULL AS varchar),cast(NULL AS varchar),cast(NULL AS varchar))
     )
-    SELECT
-        id,
-        code,
-        system,
-        display
-    FROM union_table
+        AS t ("id","code","system","display")
+    WHERE 1 = 0 -- ensure empty table
 );
 
-
 -- ###########################################################