Add BaseTableBuilder and CountsBuilder to the public API

cumulus_library/__init__.py

@@ -1,7 +1,9 @@
 """Package metadata"""
 
+from .base_table_builder import BaseTableBuilder
 from .base_utils import StudyConfig
+from .statistics.counts import CountsBuilder
 from .study_manifest import StudyManifest
 
-__all__ = ["StudyConfig", "StudyManifest"]
+__all__ = ["BaseTableBuilder", "CountsBuilder", "StudyConfig", "StudyManifest"]
 __version__ = "3.0.0"

cumulus_library/studies/core/builder_condition.py

@@ -1,4 +1,4 @@
-from cumulus_library import base_table_builder, base_utils
+import cumulus_library
 from cumulus_library.studies.core.core_templates import core_templates
 from cumulus_library.template_sql import base_templates, sql_utils
 
@@ -12,7 +12,7 @@
 }
 
 
-class CoreConditionBuilder(base_table_builder.BaseTableBuilder):
+class CoreConditionBuilder(cumulus_library.BaseTableBuilder):
     display_text = "Creating Condition tables..."
 
     def denormalize_codes(self):
@@ -75,7 +75,7 @@ def denormalize_codes(self):
     def prepare_queries(
         self,
         *args,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         **kwargs,
     ):
         self.denormalize_codes()

cumulus_library/studies/core/builder_documentreference.py

@@ -1,4 +1,4 @@
-from cumulus_library import base_table_builder, base_utils
+import cumulus_library
 from cumulus_library.studies.core.core_templates import core_templates
 from cumulus_library.template_sql import sql_utils
 
@@ -14,13 +14,13 @@
 }
 
 
-class CoreDocumentreferenceBuilder(base_table_builder.BaseTableBuilder):
+class CoreDocumentreferenceBuilder(cumulus_library.BaseTableBuilder):
     display_text = "Creating DocumentReference tables..."
 
     def prepare_queries(
         self,
         *args,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         **kwargs,
     ):
         self.queries = sql_utils.denormalize_complex_objects(

cumulus_library/studies/core/builder_encounter.py

@@ -1,6 +1,6 @@
 from dataclasses import dataclass
 
-from cumulus_library import base_table_builder, base_utils
+import cumulus_library
 from cumulus_library.studies.core.core_templates import core_templates
 from cumulus_library.template_sql import sql_utils
 
@@ -34,7 +34,7 @@ def __post_init__(self):
         self.target_table = f"core__encounter_dn_{self.column_hierarchy[-1][0]}"
 
 
-class CoreEncounterBuilder(base_table_builder.BaseTableBuilder):
+class CoreEncounterBuilder(cumulus_library.BaseTableBuilder):
     display_text = "Creating Encounter tables..."
 
     def denormalize_codes(self, database):
@@ -108,7 +108,7 @@ def denormalize_codes(self, database):
     def prepare_queries(
         self,
         *args,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         **kwargs,
     ):
         self.denormalize_codes(config.db)

cumulus_library/studies/core/builder_medicationrequest.py

@@ -1,6 +1,6 @@
 """Module for generating core medicationrequest table"""
 
-from cumulus_library import base_table_builder, base_utils
+import cumulus_library
 from cumulus_library.studies.core.core_templates import core_templates
 from cumulus_library.template_sql import sql_utils
 
@@ -19,13 +19,13 @@
 }
 
 
-class MedicationRequestBuilder(base_table_builder.BaseTableBuilder):
+class MedicationRequestBuilder(cumulus_library.BaseTableBuilder):
     display_text = "Creating MedicationRequest table..."
 
     def prepare_queries(
         self,
         *args,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         **kwargs,
     ) -> None:
         """Constructs queries related to medication requests

cumulus_library/studies/core/builder_observation.py

@@ -2,7 +2,7 @@
 
 from dataclasses import dataclass
 
-from cumulus_library import base_table_builder, base_utils
+import cumulus_library
 from cumulus_library.studies.core.core_templates import core_templates
 from cumulus_library.template_sql import sql_utils
 
@@ -36,13 +36,13 @@ def __post_init__(self):
         self.target_table = f"core__observation_{table_suffix}"
 
 
-class ObservationBuilder(base_table_builder.BaseTableBuilder):
+class ObservationBuilder(cumulus_library.BaseTableBuilder):
     display_text = "Creating Observation tables..."
 
     def prepare_queries(
         self,
         *args,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         **kwargs,
     ):
         """constructs queries related to patient extensions of interest

cumulus_library/studies/core/builder_patient.py

@@ -1,7 +1,7 @@
 """Module for extracting US core extensions from patient records"""
 
-from cumulus_library import base_utils, databases
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
+from cumulus_library import databases
 from cumulus_library.studies.core.core_templates import core_templates
 from cumulus_library.template_sql import base_templates, sql_utils
 
@@ -15,7 +15,7 @@
 }
 
 
-class PatientBuilder(BaseTableBuilder):
+class PatientBuilder(cumulus_library.BaseTableBuilder):
     display_text = "Creating Patient tables..."
 
     @staticmethod
@@ -57,7 +57,7 @@ def make_extension_query(
     def prepare_queries(
         self,
         *args,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         **kwargs,
     ):
         """constructs queries related to patient extensions of interest

cumulus_library/studies/core/builder_prereq_tables.py

@@ -6,10 +6,10 @@
 
 import sqlparse
 
-from cumulus_library import base_table_builder
+import cumulus_library
 
 
-class CorePrereqTableBuilder(base_table_builder.BaseTableBuilder):
+class CorePrereqTableBuilder(cumulus_library.BaseTableBuilder):
     display_text = "Creating core prerequisite tables..."
 
     def prepare_queries(self, *args, **kwargs):

cumulus_library/studies/core/count_core.py

@@ -1,9 +1,9 @@
 from pathlib import Path
 
-from cumulus_library.statistics import counts
+import cumulus_library
 
 
-class CoreCountsBuilder(counts.CountsBuilder):
+class CoreCountsBuilder(cumulus_library.CountsBuilder):
     display_text = "Creating core counts..."
 
     def count_core_condition(self, duration: str = "month"):
@@ -119,6 +119,6 @@ def prepare_queries(self, *args, **kwargs):
         ]
 
 
-if __name__ == "__main__":
+if __name__ == "__main__":  # pragma: no cover
     builder = CoreCountsBuilder()
     builder.write_counts(f"{Path(__file__).resolve().parent}/count_core.sql")

cumulus_library/studies/discovery/code_detection.py

@@ -1,12 +1,13 @@
 """Module for generating encounter codeableConcept table"""
 
-from cumulus_library import base_table_builder, base_utils
+import cumulus_library
+from cumulus_library import base_utils
 from cumulus_library.studies.discovery import code_definitions
 from cumulus_library.studies.discovery.discovery_templates import discovery_templates
 from cumulus_library.template_sql import sql_utils
 
 
-class CodeDetectionBuilder(base_table_builder.BaseTableBuilder):
+class CodeDetectionBuilder(cumulus_library.BaseTableBuilder):
     display_text = "Selecting unique code systems..."
 
     def _check_coding_against_db(self, code_source, database):
@@ -35,7 +36,7 @@ def _check_codes_in_fields(self, code_sources: list[dict], database) -> dict:
     def prepare_queries(
         self,
         *args,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         **kwargs,
     ):
         """Constructs queries related to condition codeableConcept

cumulus_library/studies/vocab/vocab_icd_builder.py

@@ -4,16 +4,16 @@
 
 import pandas
 
-from cumulus_library import base_table_builder, base_utils
+import cumulus_library
 from cumulus_library.template_sql import base_templates
 
 
-class VocabIcdRunner(base_table_builder.BaseTableBuilder):
+class VocabIcdRunner(cumulus_library.BaseTableBuilder):
     display_text = "Creating ICD vocab..."
 
     def prepare_queries(
         self,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         *args,
         **kwargs,
     ):

tests/test_data/study_dedicated_schema/module1.py

@@ -1,7 +1,7 @@
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 
-class ModuleOneRunner(BaseTableBuilder):
+class ModuleOneRunner(cumulus_library.BaseTableBuilder):
     display_text = "module1"
 
     def prepare_queries(self, *args, **kwargs):

tests/test_data/study_dedicated_schema/module2.py

@@ -1,7 +1,7 @@
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 
-class ModuleTwoRunner(BaseTableBuilder):
+class ModuleTwoRunner(cumulus_library.BaseTableBuilder):
     display_text = "module2"
 
     def prepare_queries(self, *args, **kwargs):

tests/test_data/study_python_counts_valid/module1.py

@@ -1,7 +1,7 @@
-from cumulus_library.statistics.counts import CountsBuilder
+import cumulus_library
 
 
-class ModuleOneRunner(CountsBuilder):
+class ModuleOneRunner(cumulus_library.CountsBuilder):
     display_text = "module1"
 
     def __init__(self):

tests/test_data/study_python_counts_valid/module2.py

@@ -1,7 +1,7 @@
-from cumulus_library.statistics.counts import CountsBuilder
+import cumulus_library
 
 
-class ModuleTwoRunner(CountsBuilder):
+class ModuleTwoRunner(cumulus_library.CountsBuilder):
     display_text = "module2"
 
     def __init__(self):

tests/test_data/study_python_local_template/module1.py

@@ -1,9 +1,9 @@
 from study_python_local_template import local_template
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 
-class ModuleOneRunner(BaseTableBuilder):
+class ModuleOneRunner(cumulus_library.BaseTableBuilder):
     display_text = "module1"
 
     def prepare_queries(self, *args, **kwargs):

tests/test_data/study_python_no_subclass/module1.py

@@ -1,7 +1,7 @@
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 
-class ModuleOneRunner(BaseTableBuilder):
+class ModuleOneRunner(cumulus_library.BaseTableBuilder):
     display_text = "Module 1"
 
     @classmethod

tests/test_data/study_python_s3/module1.py

@@ -1,7 +1,7 @@
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 
-class ModuleOneRunner(BaseTableBuilder):
+class ModuleOneRunner(cumulus_library.BaseTableBuilder):
     display_text = "module1"
 
     def prepare_queries(self, *args, **kwargs):

tests/test_data/study_python_s3/module2.py

@@ -1,7 +1,7 @@
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 
-class ModuleTwoRunner(BaseTableBuilder):
+class ModuleTwoRunner(cumulus_library.BaseTableBuilder):
     display_text = "module2"
 
     def prepare_queries(self, *args, **kwargs):

tests/test_data/study_python_valid/module1.py

@@ -1,7 +1,7 @@
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 
-class ModuleOneRunner(BaseTableBuilder):
+class ModuleOneRunner(cumulus_library.BaseTableBuilder):
     display_text = "module1"
 
     def prepare_queries(self, *args, **kwargs):

tests/test_data/study_python_valid/module2.py

@@ -1,7 +1,7 @@
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 
-class ModuleTwoRunner(BaseTableBuilder):
+class ModuleTwoRunner(cumulus_library.BaseTableBuilder):
     display_text = "module2"
 
     def prepare_queries(self, *args, **kwargs):

tests/test_discovery.py

@@ -2,6 +2,8 @@
 import pathlib
 from unittest import mock
 
+import pytest
+
 from cumulus_library import cli, databases
 from cumulus_library.studies.discovery.discovery_templates import discovery_templates
 from tests import conftest
@@ -144,3 +146,18 @@ def test_get_system_pairs():
         ],
     )
     assert query == expected
+
+
+@mock.patch.dict(os.environ, clear=True)
+@mock.patch("cumulus_library.studies.discovery.code_definitions.code_list", new=[{}])
+def test_bad_code_definition(tmp_path):
+    with pytest.raises(KeyError, match="Expected table_name and column_hierarchy keys"):
+        cli.main(
+            cli_args=conftest.duckdb_args(
+                [
+                    "build",
+                    "--target=discovery",
+                ],
+                tmp_path,
+            )
+        )