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Fix sqlmodel 🚀
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@motey
motey committed Nov 8, 2024
1 parent 8d871b6 commit 640f417
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Showing 12 changed files with 489 additions and 386 deletions.
12 changes: 0 additions & 12 deletions DZDOMOPModel/examples/sqlite_insert_person_sqlmodel_wip.py
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@@ -1,17 +1,5 @@
from sqlmodel import SQLModel, Session, create_engine

#### THIS IS WORK IN PROGRESS AND NOT WORKING ###
#### PLEASE IGNORE ME ###


if __name__ == "__main__":
from pathlib import Path
import sys, os

MODULE_DIR = Path(__file__).parent
MODULE_PARENT_DIR = MODULE_DIR.parent.absolute()
sys.path.insert(0, os.path.normpath(MODULE_PARENT_DIR))


from omopmodel import OMOP_5_4_sqlmodels as omop54

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20 changes: 9 additions & 11 deletions DZDOMOPModel/omopmodel/OMOP_5_3_dataclasses.py
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Expand Up @@ -80,7 +80,7 @@ class Concept(Base):
concept_class: Mapped['ConceptClass'] = relationship('ConceptClass', foreign_keys=[concept_class_id], back_populates='concept')
domain: Mapped['Domain'] = relationship('Domain', foreign_keys=[domain_id], back_populates='concept')
vocabulary: Mapped['Vocabulary'] = relationship('Vocabulary', foreign_keys=[vocabulary_id], back_populates='concept')
concept_class_: Mapped[List['ConceptClass']] = relationship('ConceptClass', foreign_keys='[ConceptClass.concept_class_concept_id]', back_populates='concept_class_concept')
concept_classes: Mapped[List['ConceptClass']] = relationship('ConceptClass', foreign_keys='[ConceptClass.concept_class_concept_id]', back_populates='concept_class_concept')


class ConceptClass(Base):
Expand Down Expand Up @@ -530,8 +530,8 @@ class FactRelationship(Base):
fact_id_2: Mapped[int] = mapped_column(Integer, )
relationship_concept_id: Mapped[int] = mapped_column(Integer, )

concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[domain_concept_id_1])
concept_: Mapped['Concept'] = relationship('Concept', foreign_keys=[domain_concept_id_2])
domain_concept_1: Mapped['Concept'] = relationship('Concept', foreign_keys=[domain_concept_id_1])
domain_concept_2: Mapped['Concept'] = relationship('Concept', foreign_keys=[domain_concept_id_2])
relationship_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[relationship_concept_id])


Expand Down Expand Up @@ -672,8 +672,8 @@ class ConceptRelationship(Base):
valid_end_date: Mapped[datetime.date] = mapped_column(Date, comment='USER GUIDANCE: The date when the relationship is invalidated.')
invalid_reason: Mapped[Optional[str]] = mapped_column(String(1), comment='USER GUIDANCE: Reason the relationship was invalidated. Possible values are "D" (deleted), "U" (updated) or NULL. ')

concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[concept_id_1])
concept_: Mapped['Concept'] = relationship('Concept', foreign_keys=[concept_id_2])
concept_1: Mapped['Concept'] = relationship('Concept', foreign_keys=[concept_id_1])
concept_2: Mapped['Concept'] = relationship('Concept', foreign_keys=[concept_id_2])
relationship_: Mapped['Relationship'] = relationship('Relationship', back_populates='concept_relationship')


Expand Down Expand Up @@ -1254,8 +1254,7 @@ class VisitOccurrence(Base):
care_site: Mapped['CareSite'] = relationship('CareSite', back_populates='visit_occurrence')
discharge_to_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[discharge_to_concept_id])
person: Mapped['Person'] = relationship('Person', back_populates='visit_occurrence')
preceding_visit_occurrence: Mapped['VisitOccurrence'] = relationship('VisitOccurrence', remote_side=[visit_occurrence_id], back_populates='preceding_visit_occurrence_reverse')
preceding_visit_occurrence_reverse: Mapped[List['VisitOccurrence']] = relationship('VisitOccurrence', remote_side=[preceding_visit_occurrence_id], back_populates='preceding_visit_occurrence')
preceding_visit_occurrence: Mapped['VisitOccurrence'] = relationship('VisitOccurrence', remote_side=[visit_occurrence_id])
provider: Mapped['Provider'] = relationship('Provider', back_populates='visit_occurrence')
visit_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_concept_id])
visit_source_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_source_concept_id])
Expand Down Expand Up @@ -1348,12 +1347,10 @@ class VisitDetail(Base):
care_site: Mapped['CareSite'] = relationship('CareSite', back_populates='visit_detail')
discharge_to_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[discharge_to_concept_id])
person: Mapped['Person'] = relationship('Person', back_populates='visit_detail')
preceding_visit_detail: Mapped['VisitDetail'] = relationship('VisitDetail', remote_side=[visit_detail_id], foreign_keys=[preceding_visit_detail_id], back_populates='preceding_visit_detail_reverse')
preceding_visit_detail_reverse: Mapped[List['VisitDetail']] = relationship('VisitDetail', remote_side=[preceding_visit_detail_id], foreign_keys=[preceding_visit_detail_id], back_populates='preceding_visit_detail')
preceding_visit_detail: Mapped['VisitDetail'] = relationship('VisitDetail', remote_side=[visit_detail_id], foreign_keys=[preceding_visit_detail_id])
provider: Mapped['Provider'] = relationship('Provider', back_populates='visit_detail')
visit_detail_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_detail_concept_id])
visit_detail_parent: Mapped['VisitDetail'] = relationship('VisitDetail', remote_side=[visit_detail_id], foreign_keys=[visit_detail_parent_id], back_populates='visit_detail_parent_reverse')
visit_detail_parent_reverse: Mapped[List['VisitDetail']] = relationship('VisitDetail', remote_side=[visit_detail_parent_id], foreign_keys=[visit_detail_parent_id], back_populates='visit_detail_parent')
visit_detail_parent: Mapped['VisitDetail'] = relationship('VisitDetail', remote_side=[visit_detail_id], foreign_keys=[visit_detail_parent_id])
visit_detail_source_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_detail_source_concept_id])
visit_detail_type_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_detail_type_concept_id])
visit_occurrence: Mapped['VisitOccurrence'] = relationship('VisitOccurrence', back_populates='visit_detail')
Expand Down Expand Up @@ -1836,3 +1833,4 @@ class Observation(Base):




20 changes: 9 additions & 11 deletions DZDOMOPModel/omopmodel/OMOP_5_3_declarative.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ class Concept(Base):
concept_class: Mapped['ConceptClass'] = relationship('ConceptClass', foreign_keys=[concept_class_id], back_populates='concept')
domain: Mapped['Domain'] = relationship('Domain', foreign_keys=[domain_id], back_populates='concept')
vocabulary: Mapped['Vocabulary'] = relationship('Vocabulary', foreign_keys=[vocabulary_id], back_populates='concept')
concept_class_: Mapped[List['ConceptClass']] = relationship('ConceptClass', foreign_keys='[ConceptClass.concept_class_concept_id]', back_populates='concept_class_concept')
concept_classes: Mapped[List['ConceptClass']] = relationship('ConceptClass', foreign_keys='[ConceptClass.concept_class_concept_id]', back_populates='concept_class_concept')


class ConceptClass(Base):
Expand Down Expand Up @@ -530,8 +530,8 @@ class FactRelationship(Base):
fact_id_2: Mapped[int] = mapped_column(Integer, )
relationship_concept_id: Mapped[int] = mapped_column(Integer, )

concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[domain_concept_id_1])
concept_: Mapped['Concept'] = relationship('Concept', foreign_keys=[domain_concept_id_2])
domain_concept_1: Mapped['Concept'] = relationship('Concept', foreign_keys=[domain_concept_id_1])
domain_concept_2: Mapped['Concept'] = relationship('Concept', foreign_keys=[domain_concept_id_2])
relationship_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[relationship_concept_id])


Expand Down Expand Up @@ -672,8 +672,8 @@ class ConceptRelationship(Base):
valid_end_date: Mapped[datetime.date] = mapped_column(Date, comment='USER GUIDANCE: The date when the relationship is invalidated.')
invalid_reason: Mapped[Optional[str]] = mapped_column(String(1), comment='USER GUIDANCE: Reason the relationship was invalidated. Possible values are "D" (deleted), "U" (updated) or NULL. ')

concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[concept_id_1])
concept_: Mapped['Concept'] = relationship('Concept', foreign_keys=[concept_id_2])
concept_1: Mapped['Concept'] = relationship('Concept', foreign_keys=[concept_id_1])
concept_2: Mapped['Concept'] = relationship('Concept', foreign_keys=[concept_id_2])
relationship_: Mapped['Relationship'] = relationship('Relationship', back_populates='concept_relationship')


Expand Down Expand Up @@ -1254,8 +1254,7 @@ class VisitOccurrence(Base):
care_site: Mapped['CareSite'] = relationship('CareSite', back_populates='visit_occurrence')
discharge_to_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[discharge_to_concept_id])
person: Mapped['Person'] = relationship('Person', back_populates='visit_occurrence')
preceding_visit_occurrence: Mapped['VisitOccurrence'] = relationship('VisitOccurrence', remote_side=[visit_occurrence_id], back_populates='preceding_visit_occurrence_reverse')
preceding_visit_occurrence_reverse: Mapped[List['VisitOccurrence']] = relationship('VisitOccurrence', remote_side=[preceding_visit_occurrence_id], back_populates='preceding_visit_occurrence')
preceding_visit_occurrence: Mapped['VisitOccurrence'] = relationship('VisitOccurrence', remote_side=[visit_occurrence_id])
provider: Mapped['Provider'] = relationship('Provider', back_populates='visit_occurrence')
visit_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_concept_id])
visit_source_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_source_concept_id])
Expand Down Expand Up @@ -1348,12 +1347,10 @@ class VisitDetail(Base):
care_site: Mapped['CareSite'] = relationship('CareSite', back_populates='visit_detail')
discharge_to_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[discharge_to_concept_id])
person: Mapped['Person'] = relationship('Person', back_populates='visit_detail')
preceding_visit_detail: Mapped['VisitDetail'] = relationship('VisitDetail', remote_side=[visit_detail_id], foreign_keys=[preceding_visit_detail_id], back_populates='preceding_visit_detail_reverse')
preceding_visit_detail_reverse: Mapped[List['VisitDetail']] = relationship('VisitDetail', remote_side=[preceding_visit_detail_id], foreign_keys=[preceding_visit_detail_id], back_populates='preceding_visit_detail')
preceding_visit_detail: Mapped['VisitDetail'] = relationship('VisitDetail', remote_side=[visit_detail_id], foreign_keys=[preceding_visit_detail_id])
provider: Mapped['Provider'] = relationship('Provider', back_populates='visit_detail')
visit_detail_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_detail_concept_id])
visit_detail_parent: Mapped['VisitDetail'] = relationship('VisitDetail', remote_side=[visit_detail_id], foreign_keys=[visit_detail_parent_id], back_populates='visit_detail_parent_reverse')
visit_detail_parent_reverse: Mapped[List['VisitDetail']] = relationship('VisitDetail', remote_side=[visit_detail_parent_id], foreign_keys=[visit_detail_parent_id], back_populates='visit_detail_parent')
visit_detail_parent: Mapped['VisitDetail'] = relationship('VisitDetail', remote_side=[visit_detail_id], foreign_keys=[visit_detail_parent_id])
visit_detail_source_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_detail_source_concept_id])
visit_detail_type_concept: Mapped['Concept'] = relationship('Concept', foreign_keys=[visit_detail_type_concept_id])
visit_occurrence: Mapped['VisitOccurrence'] = relationship('VisitOccurrence', back_populates='visit_detail')
Expand Down Expand Up @@ -1836,3 +1833,4 @@ class Observation(Base):




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