Refactor of get chart data endpoint

.github/workflows/ci.yaml

@@ -53,6 +53,9 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install ".[dev]"
+      - name: Run sqlfluff on jinja templates
+        run: |
+          sqlfluff lint
       - name: Run ruff
         if: success() || failure() # still run ruff if above checks fails
         run: |

.sqlfluff

@@ -0,0 +1,49 @@
+[sqlfluff]
+templater = jinja
+dialect = athena
+sql_file_exts = .sql,.sql.jinja
+exclude_rules=
+    # these rule overfires on athena nested arrays
+    references.from,
+    structure.column_order,
+    aliasing.unused,
+    # this rule interferes with FHIR naming conventions
+    capitalisation.identifiers
+max_line_length = 90
+
+[sqlfluff:rules:layout.long_lines]
+ignore_comment_lines = true
+
+[sqlfluff:rules:capitalisation.keywords]
+capitalisation_policy = upper
+
+
+[sqlfluff:templater:jinja]
+load_macros_from_path = src/dashboard/get_chart_data/templates
+
+[sqlfluff:templater:jinja:context]
+data_column = 'foo'
+stratifier_column= 'bar'
+count_columns=['cnt']
+schema='schema'
+data_package_id='study__table__001'
+coalesce_columns=['baz','foobar']
+inline_configs=[
+        [
+            {'data':'foo','type': 'matches': 'a'},
+            {'data':'foo','type': 'matches': 'b'}
+        ],
+        [
+            {'data':'baz','type': 'eq', 'matches': '1'}, 
+            {'data':'baz','type': 'isNull'} 
+        ]
+    ]
+none_configs=[
+        [
+            {'data':'foo','type': 'matches': 'a'},
+            {'data':'foo','type': 'matches': 'b'}
+        ],
+        [
+            {'data':'baz','type': 'isNull'} 
+        ]
+    ]

pyproject.toml

@@ -9,6 +9,7 @@ dependencies= [
     "arrow >=1.2.3",
     "awswrangler >=3.5, <4",
     "boto3",
+    "Jinja2 >=3.1.4, <4",
     "pandas >=2, <3",
     "requests", # scripts only
     "rich",
@@ -48,8 +49,9 @@ test = [
     "pytest-mock"
 ]
 dev = [
-    "ruff < 0.6",
     "pre-commit",
+    "ruff < 0.6",
+    "sqlfluff >= 3.2.5"
 ]
 
 [tool.coverage.run]