omop-constructs 0.2.16__tar.gz → 0.3.0__tar.gz

{omop_constructs-0.2.16 → omop_constructs-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: omop-constructs
-Version: 0.2.16
+Version: 0.3.0
 Summary: For building complex constructs on top of the omop-alchemy library.
 Author: Georgie Kennedy
 Author-email: Georgie Kennedy <georgina.kennedy@unsw.edu.au>

{omop_constructs-0.2.16 → omop_constructs-0.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.2.16"
+version = "0.3.0"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [

{omop_constructs-0.2.16 → omop_constructs-0.3.0}/src/omop_constructs/alchemy/modifiers/__init__.py

@@ -6,7 +6,8 @@ from .modifier_mappers import (
     GradeModifierMV, 
     LateralityModifierMV, 
     SizeModifierMV,
-    MetastaticDiseaseModifierMV
+    MetastaticDiseaseModifierMV,
+    AllStageModifierMV
 )
 from .condition_modifier_mv import ModifiedCondition
 
@@ -19,5 +20,6 @@ __all__ = [
     "LateralityModifierMV",
     "SizeModifierMV",
     "ModifiedCondition",
-    "MetastaticDiseaseModifierMV"
+    "MetastaticDiseaseModifierMV",
+    "AllStageModifierMV"
 ]

{omop_constructs-0.2.16 → omop_constructs-0.3.0}/src/omop_constructs/alchemy/modifiers/condition_modifier_join.py

@@ -13,7 +13,8 @@ from .modifier_mappers import (
     GradeModifierMV,
     SizeModifierMV,
     LateralityModifierMV,
-    MetastaticDiseaseModifierMV
+    MetastaticDiseaseModifierMV,
+    AllStageModifierMV
 )
 
 condition_concept = so.aliased(Concept, name='condition_concept')
@@ -125,5 +126,47 @@ modified_conditions_join = (
         ),
         isouter=True
     )
+    .join(
+        MetastaticDiseaseModifierMV, 
+        sa.and_(
+            MetastaticDiseaseModifierMV.meas_event_field_concept_id==runtime.modifiers.modifier_fields.condition_occurrence_id,
+            Condition_Occurrence.condition_occurrence_id==MetastaticDiseaseModifierMV.measurement_event_id
+        ),
+        isouter=True
+    )
+    .join(condition_concept, condition_concept.concept_id==Condition_Occurrence.condition_concept_id)
+)
+
+all_stage_join = (
+    sa.select(
+        sa.func.row_number().over().label('mv_id'),
+        Condition_Occurrence.person_id,
+        Condition_Occurrence.condition_start_date, 
+        Condition_Occurrence.condition_occurrence_id,
+        Condition_Occurrence.condition_source_value,
+        Condition_Occurrence.condition_concept_id,
+        condition_concept.concept_name.label('condition_concept'),
+        Episode_Event.episode_id.label('condition_episode'),
+    	AllStageModifierMV.stage_id.label('stage_id'),
+    	AllStageModifierMV.stage_date.label('stage_date'),
+    	AllStageModifierMV.stage_concept_id.label('stage_concept_id'),
+    	AllStageModifierMV.stage_label.label('stage_label'),
+    )
+    .join(
+        Episode_Event, 
+        sa.and_(
+            Episode_Event.event_id==Condition_Occurrence.condition_occurrence_id,
+            Episode_Event.episode_event_field_concept_id==runtime.modifiers.modifier_fields.condition_occurrence_id
+        ),
+        isouter=True
+    )
+    .join(
+        AllStageModifierMV, 
+        sa.and_(
+            AllStageModifierMV.meas_event_field_concept_id==runtime.modifiers.modifier_fields.condition_occurrence_id,
+            Condition_Occurrence.condition_occurrence_id==AllStageModifierMV.measurement_event_id
+        ),
+        isouter=True
+    )
     .join(condition_concept, condition_concept.concept_id==Condition_Occurrence.condition_concept_id)
-)
+)

omop_constructs-0.3.0/src/omop_constructs/alchemy/modifiers/condition_modifier_mv.py

@@ -0,0 +1,102 @@
+import sqlalchemy as sa
+from orm_loader.helpers import Base
+from .condition_modifier_join import modified_conditions_join,  all_stage_join
+from ...core.materialized import MaterializedViewMixin
+from ...core.constructs import register_construct
+from .modifier_mappers import (
+    TStageMV, 
+    NStageMV, 
+    MStageMV,   
+    GroupStageMV,
+    GradeModifierMV,
+    SizeModifierMV,
+    LateralityModifierMV,
+    MetastaticDiseaseModifierMV,
+    AllStageModifierMV
+)
+
+@register_construct
+class StageModifier(MaterializedViewMixin, Base):
+    """
+    this class contains all stage modifier records no matter the sub-type, nor does it preference 
+    clin / path stage etc - just a dump of all, along with the identifier to link to condition ep
+    """
+    __mv_name__ = 'stage_modifier_mv'
+    __mv_select__ = all_stage_join.select()
+    __mv_pk__ = ["stage_id"]
+    __table_args__ = {"extend_existing": True}
+    __tablename__ = __mv_name__
+    __deps__ = (
+        AllStageModifierMV.__mv_name__,
+     )
+    mv_id = sa.Column(primary_key=True)
+    person_id = sa.Column(sa.Integer)
+    condition_start_date = sa.Column(sa.Date)
+    condition_occurrence_id = sa.Column(sa.Integer)
+    condition_source_value = sa.Column(sa.String)
+    condition_concept_id = sa.Column(sa.Integer)
+    condition_concept = sa.Column(sa.String)
+    condition_episode = sa.Column(sa.Integer)
+    stage_id = sa.Column(sa.Integer)
+    stage_date = sa.Column(sa.Date)
+    stage_concept_id = sa.Column(sa.Integer)
+    stage_label = sa.Column(sa.String)
+
+@register_construct
+class ModifiedCondition(MaterializedViewMixin, Base):
+    __mv_name__ = 'modified_conditions_mv'
+    __mv_select__ = modified_conditions_join.select()
+    __mv_pk__ = ["mv_id"]
+    __table_args__ = {"extend_existing": True}
+    __tablename__ = __mv_name__
+    __deps__ = (
+        TStageMV.__mv_name__,
+        NStageMV.__mv_name__,
+        MStageMV.__mv_name__,
+        GroupStageMV.__mv_name__,
+        GradeModifierMV.__mv_name__,
+        SizeModifierMV.__mv_name__,
+        LateralityModifierMV.__mv_name__,
+        MetastaticDiseaseModifierMV.__mv_name__
+    )
+
+    mv_id = sa.Column(primary_key=True)
+    person_id = sa.Column(sa.Integer)
+    condition_start_date = sa.Column(sa.Date)
+    condition_occurrence_id = sa.Column(sa.Integer)
+    condition_source_value = sa.Column(sa.String)
+    condition_concept_id = sa.Column(sa.Integer)
+    condition_concept = sa.Column(sa.String)
+    condition_episode = sa.Column(sa.Integer)
+    t_stage_id = sa.Column(sa.Integer)
+    t_stage_date = sa.Column(sa.Date)
+    t_stage_concept_id = sa.Column(sa.Integer)
+    t_stage_label = sa.Column(sa.String)
+    n_stage_id = sa.Column(sa.Integer)
+    n_stage_date = sa.Column(sa.Date)
+    n_stage_concept_id = sa.Column(sa.Integer)
+    n_stage_label = sa.Column(sa.String)
+    m_stage_id = sa.Column(sa.Integer)
+    m_stage_date = sa.Column(sa.Date)
+    m_stage_concept_id = sa.Column(sa.Integer)
+    m_stage_label = sa.Column(sa.String)
+    group_stage_id = sa.Column(sa.Integer)
+    group_stage_date = sa.Column(sa.Date)
+    group_stage_concept_id = sa.Column(sa.Integer)
+    group_stage_label = sa.Column(sa.String)
+    grade_id = sa.Column(sa.Integer)
+    grade_date = sa.Column(sa.Date)
+    grade_concept_id = sa.Column(sa.Integer)
+    grade_label = sa.Column(sa.String)
+    size_id = sa.Column(sa.Integer)
+    size_date = sa.Column(sa.Date)
+    size_concept_id = sa.Column(sa.Integer)
+    size_label = sa.Column(sa.String)
+    laterality_id = sa.Column(sa.Integer)
+    laterality_date = sa.Column(sa.Date)
+    laterality_concept_id = sa.Column(sa.Integer)
+    laterality_label = sa.Column(sa.String)
+    metastatic_disease_id = sa.Column(sa.Integer)
+    metastatic_disease_date = sa.Column(sa.Date)
+    metastatic_disease_concept_id = sa.Column(sa.Integer)
+    metastatic_disease_label = sa.Column(sa.String)

{omop_constructs-0.2.16 → omop_constructs-0.3.0}/src/omop_constructs/alchemy/modifiers/modifier_joins.py

@@ -40,4 +40,14 @@ grade_select = earliest_modifier(
 mets_select = earliest_modifier(
     get_direct_modifier_query(list(registry['metastatic_disease'].all_concepts), name="metastatic_disease"),
     name="metastatic_disease_earliest"
+)
+
+all_stage_select = get_direct_modifier_query(
+    (
+        list(
+                registry['tnm_t_stage'].all_concepts | registry['tnm_n_stage'].all_concepts | 
+                registry['tnm_m_stage'].all_concepts | registry['tnm_group_stage'].all_concepts
+            )
+    ),
+    name="all_stage_modifiers"
 )

{omop_constructs-0.2.16 → omop_constructs-0.3.0}/src/omop_constructs/alchemy/modifiers/modifier_mappers.py

@@ -8,7 +8,8 @@ from .modifier_joins import (
     laterality_select,
     size_select,
     grade_select,
-    mets_select
+    mets_select,
+    all_stage_select
 )
 from ...core.materialized import MaterializedViewMixin
 from ...core.constructs import register_construct
@@ -113,3 +114,12 @@ class MetastaticDiseaseModifierMV(MeasModCols, MaterializedViewMixin, Base):
     __tablename__ = __mv_name__
     value_as_concept_id = sa.Column(sa.Integer)
     measurement_concept_id = sa.Column(sa.Integer)
+
+@register_construct
+class AllStageModifierMV(StageColumns, MaterializedViewMixin, Base):
+    __mv_name__ = "all_stage_modifier_mv"
+    __mv_select__ = all_stage_select.select()
+    __mv_index__ = "measurement_event_id"
+    __deps__ = ()
+    __tablename__ = __mv_name__
+    measurement_concept_id = sa.Column(sa.Integer)

omop_constructs-0.2.16/src/omop_constructs/alchemy/modifiers/condition_modifier_mv.py

@@ -1,56 +0,0 @@
-import sqlalchemy as sa
-from orm_loader.helpers import Base
-from .condition_modifier_join import modified_conditions_join
-from ...core.materialized import MaterializedViewMixin
-from ...core.constructs import register_construct
-from .modifier_mappers import (
-    TStageMV, 
-    NStageMV, 
-    MStageMV,   
-    GroupStageMV,
-    GradeModifierMV,
-    SizeModifierMV,
-    LateralityModifierMV
-)
-
-@register_construct
-class ModifiedCondition(MaterializedViewMixin, Base):
-    __mv_name__ = 'modified_conditions_mv'
-    __mv_select__ = modified_conditions_join.select()
-    __mv_pk__ = ["mv_id"]
-    __table_args__ = {"extend_existing": True}
-    __tablename__ = __mv_name__
-    __deps__ = (
-        TStageMV.__mv_name__,
-        NStageMV.__mv_name__,
-        MStageMV.__mv_name__,
-        GroupStageMV.__mv_name__,
-        GradeModifierMV.__mv_name__,
-        SizeModifierMV.__mv_name__,
-        LateralityModifierMV.__mv_name__,
-    )
-
-    mv_id = sa.Column(primary_key=True)
-    person_id = sa.Column(sa.Integer)
-    condition_start_date = sa.Column(sa.Date)
-    condition_occurrence_id = sa.Column(sa.Integer)
-    condition_source_value = sa.Column(sa.String)
-    condition_concept_id = sa.Column(sa.Integer)
-    condition_concept = sa.Column(sa.String)
-    condition_episode = sa.Column(sa.Integer)
-    stage_id = sa.Column(sa.Integer)
-    stage_date = sa.Column(sa.Date)
-    stage_concept_id = sa.Column(sa.Integer)
-    stage_label = sa.Column(sa.String)
-    grade_id = sa.Column(sa.Integer)
-    grade_date = sa.Column(sa.Date)
-    grade_concept_id = sa.Column(sa.Integer)
-    grade_label = sa.Column(sa.String)
-    size_id = sa.Column(sa.Integer)
-    size_date = sa.Column(sa.Date)
-    size_concept_id = sa.Column(sa.Integer)
-    size_label = sa.Column(sa.String)
-    laterality_id = sa.Column(sa.Integer)
-    laterality_date = sa.Column(sa.Date)
-    laterality_concept_id = sa.Column(sa.Integer)
-    laterality_label = sa.Column(sa.String)