Merge pull request #59 from smart-on-fhir/mikix/library3

Update to cumulus-library 3.0

.github/workflows/ci.yaml

@@ -20,7 +20,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install dependencies
         run: |
@@ -39,7 +39,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install linters
         run: |

cumulus_library_data_metrics/__init__.py

@@ -1,3 +1,3 @@
 """Data Metrics study for Cumulus Library"""
 
-__version__ = "4.0.2"
+__version__ = "5.0.0"

cumulus_library_data_metrics/base.py

@@ -5,8 +5,8 @@
 import sys
 from typing import ClassVar
 
+import cumulus_library
 import jinja2
-from cumulus_library import base_utils
 from cumulus_library.template_sql import sql_utils
 
 from cumulus_library_data_metrics import resource_info
@@ -78,7 +78,7 @@ def _clear_deep_docref_date(self, field: str) -> None:
         if not self.schemas["DocumentReference"]["context"]["period"][field]:
             self.date_fields["DocumentReference"].remove(f"context.period.{field}")
 
-    def _query_schema(self, config: base_utils.StudyConfig) -> None:
+    def _query_schema(self, config: cumulus_library.StudyConfig) -> None:
         fields_to_check = copy.deepcopy(self.uses_fields)
 
         # Check for some known deep fields especially - if the list of fields grows, we should
@@ -93,7 +93,7 @@ def _query_schema(self, config: base_utils.StudyConfig) -> None:
         if check_docref_end:
             self._clear_deep_docref_date("end")
 
-    def extra_schema_checks(self, config: base_utils.StudyConfig) -> None:
+    def extra_schema_checks(self, config: cumulus_library.StudyConfig) -> None:
         pass
 
     def add_metric_queries(self) -> None:
@@ -102,17 +102,17 @@ def add_metric_queries(self) -> None:
     def prepare_queries(
         self,
         *args,
-        config: base_utils.StudyConfig,
+        config: cumulus_library.StudyConfig,
         **kwargs,
     ) -> None:
         self.output_mode = self.get_output_mode(config)
         self._query_schema(config)
         self.extra_schema_checks(config)
         self.add_metric_queries()
 
-    def get_output_mode(self, config: base_utils.StudyConfig) -> str:
+    def get_output_mode(self, config: cumulus_library.StudyConfig) -> str:
         output_mode = (
-            (config.options and config.options.get("output-mode"))
+            config.options.get("output-mode")
             # Deprecated approach (before --option existed) -- let it lie for now
             or os.environ.get("DATA_METRICS_OUTPUT_MODE")
         )

cumulus_library_data_metrics/c_pt_count/c_pt_count.py

@@ -2,12 +2,12 @@
 
 from typing import ClassVar
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class PatientCountBuilder(MetricMixin, BaseTableBuilder):
+class PatientCountBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "c_pt_count"
     uses_fields: ClassVar[dict] = {
         "Patient": {

cumulus_library_data_metrics/c_pt_deceased_count/c_pt_deceased_count.py

@@ -1,11 +1,11 @@
 """Module for generating c_pt_deceased_count tables"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class DeceasedCountBuilder(MetricMixin, BaseTableBuilder):
+class DeceasedCountBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "c_pt_deceased_count"
 
     def add_metric_queries(self, *args, **kwargs) -> None:

cumulus_library_data_metrics/c_resource_count/c_resource_count.py

@@ -1,12 +1,12 @@
 """Module for generating c_resource_count tables"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics import resource_info
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class ResourceCountBuilder(MetricMixin, BaseTableBuilder):
+class ResourceCountBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "c_resource_count"
 
     def make_tables(self, src: str) -> None:

cumulus_library_data_metrics/c_resources_per_pt/c_resources_per_pt.py

@@ -1,12 +1,12 @@
 """Module for generating c_resources_per_pt tables"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics import resource_info
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class ResourcesPerPatientBuilder(MetricMixin, BaseTableBuilder):
+class ResourcesPerPatientBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "c_resources_per_pt"
 
     def add_metric_queries(self) -> None:

cumulus_library_data_metrics/c_system_use/c_system_use.py

@@ -1,6 +1,6 @@
 """Module for generating c_system_use tables"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics import systems
 from cumulus_library_data_metrics.base import MetricMixin
@@ -10,7 +10,7 @@
 # We already had to drop one planned column (has_text) from it due to performance.
 
 
-class SystemUseBuilder(MetricMixin, BaseTableBuilder):
+class SystemUseBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "c_system_use"
 
     def make_table(self, **kwargs) -> None:

cumulus_library_data_metrics/c_us_core_v4_count/c_us_core_v4_count.py

@@ -1,11 +1,11 @@
 """Module for generating c_us_core_v4_count tables"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.us_core_v4 import UsCoreV4Mixin
 
 
-class UsCoreV4CountBuilder(UsCoreV4Mixin, BaseTableBuilder):
+class UsCoreV4CountBuilder(UsCoreV4Mixin, cumulus_library.BaseTableBuilder):
     name = "c_us_core_v4_count"
 
     def make_table(self, **kwargs) -> None:

cumulus_library_data_metrics/manifest.toml

@@ -41,7 +41,7 @@ export_list = [
     "data_metrics__count_c_resource_count_patient_all",
     "data_metrics__count_c_resource_count_procedure_month",
     "data_metrics__count_c_resource_count_procedure_year",
-    #"data_metrics__c_resources_per_pt_summary",  # disabled until library 3.0
+    "data_metrics__c_resources_per_pt_summary",
     "data_metrics__count_c_system_use_allergyintolerance_code",
     "data_metrics__count_c_system_use_condition_code",
     "data_metrics__count_c_system_use_device_type",
@@ -87,9 +87,9 @@ export_list = [
     "data_metrics__count_c_us_core_v4_count_patient_must_support",
     "data_metrics__count_c_us_core_v4_count_procedure_mandatory",
     "data_metrics__count_c_us_core_v4_count_procedure_must_support",
-    #"data_metrics__q_date_recent_summary",  # disabled until library 3.0
-    #"data_metrics__q_ref_target_pop_summary",  # disabled until library 3.0
-    #"data_metrics__q_ref_target_valid_summary",  # disabled until library 3.0
-    #"data_metrics__q_system_use_summary",  # disabled until library 3.0
-    #"data_metrics__q_valid_us_core_v4_summary",  # disabled until library 3.0
+    "data_metrics__q_date_recent_summary",
+    "data_metrics__q_ref_target_pop_summary",
+    "data_metrics__q_ref_target_valid_summary",
+    "data_metrics__q_system_use_summary",
+    "data_metrics__q_valid_us_core_v4_summary",
 ]

cumulus_library_data_metrics/meta/meta.py

@@ -1,11 +1,11 @@
 """Sets study metadata"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class MetadataBuilder(MetricMixin, BaseTableBuilder):
+class MetadataBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "meta"
 
     def add_date_query(self) -> None:

cumulus_library_data_metrics/q_date_recent/q_date_recent.py

@@ -2,12 +2,12 @@
 Module for generating q_date_recent tables
 """
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class DateRecentBuilder(MetricMixin, BaseTableBuilder):
+class DateRecentBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "q_date_recent"
 
     def make_table(self, **kwargs) -> None:

cumulus_library_data_metrics/q_ref_target_pop/q_ref_target_pop.py

@@ -1,11 +1,11 @@
 """Module for generating q_ref_target_pop tables"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class TargetPopBuilder(MetricMixin, BaseTableBuilder):
+class TargetPopBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "q_ref_target_pop"
 
     def make_table(self, **kwargs) -> str:

cumulus_library_data_metrics/q_ref_target_valid/q_ref_target_valid.py

@@ -2,12 +2,12 @@
 
 from typing import ClassVar
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class TargetValidBuilder(MetricMixin, BaseTableBuilder):
+class TargetValidBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "q_ref_target_valid"
 
     uses_fields: ClassVar[dict] = {

cumulus_library_data_metrics/q_system_use/q_system_use.py

@@ -1,12 +1,12 @@
 """Module for generating q_system_use tables"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics import systems
 from cumulus_library_data_metrics.base import MetricMixin
 
 
-class SystemUseBuilder(MetricMixin, BaseTableBuilder):
+class SystemUseBuilder(MetricMixin, cumulus_library.BaseTableBuilder):
     name = "q_system_use"
 
     def make_table(self, **kwargs) -> None:

cumulus_library_data_metrics/q_valid_us_core_v4/q_valid_us_core_v4.py

@@ -1,11 +1,11 @@
 """Module for generating q_valid_us_core_v4 tables"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.us_core_v4 import UsCoreV4Mixin
 
 
-class ValidUsCoreV4Builder(UsCoreV4Mixin, BaseTableBuilder):
+class ValidUsCoreV4Builder(UsCoreV4Mixin, cumulus_library.BaseTableBuilder):
     name = "q_valid_us_core_v4"
 
     def make_table(self, **kwargs) -> None:

cumulus_library_data_metrics/t_us_core_v4/t_us_core_v4.py

@@ -1,11 +1,11 @@
 """Fake/test metric for us_core_v4 profiles"""
 
-from cumulus_library.base_table_builder import BaseTableBuilder
+import cumulus_library
 
 from cumulus_library_data_metrics.us_core_v4 import UsCoreV4Mixin
 
 
-class TestUsCoreV4Builder(UsCoreV4Mixin, BaseTableBuilder):
+class TestUsCoreV4Builder(UsCoreV4Mixin, cumulus_library.BaseTableBuilder):
     name = "t_us_core_v4"
 
     def make_table(self, **kwargs) -> None:

pyproject.toml

@@ -1,8 +1,8 @@
 [project]
 name = "cumulus-library-data-metrics"
-requires-python = ">= 3.10"
+requires-python = ">= 3.11"
 dependencies = [
-    "cumulus-library >= 2.3, < 3",
+    "cumulus-library >= 3, < 4",
 ]
 description = "Data quality and characterization metrics for Cumulus"
 readme = "README.md"