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nmdc_server/migrations/versions/613956d85ada_index_study_id.py

@@ -0,0 +1,43 @@
+"""index-study-id
+
+Revision ID: 613956d85ada
+Revises: b4b234bd55cf
+Create Date: 2024-04-11 19:33:18.337288
+
+"""
+
+from typing import Optional
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "613956d85ada"
+down_revision: Optional[str] = "b4b234bd55cf"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_index(op.f("ix_biosample_id"), "biosample", ["id"], unique=False)
+    op.create_index(op.f("ix_biosample_study_id"), "biosample", ["study_id"], unique=False)
+    op.create_index(op.f("ix_omics_processing_id"), "omics_processing", ["id"], unique=False)
+    op.create_index(
+        op.f("ix_omics_processing_study_id"), "omics_processing", ["study_id"], unique=False
+    )
+    op.create_index(op.f("ix_study_id"), "study", ["id"], unique=False)
+    op.create_unique_constraint(
+        op.f("uq_submission_role_submission_id"), "submission_role", ["submission_id", "user_orcid"]
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint(op.f("uq_submission_role_submission_id"), "submission_role", type_="unique")
+    op.drop_index(op.f("ix_study_id"), table_name="study")
+    op.drop_index(op.f("ix_omics_processing_study_id"), table_name="omics_processing")
+    op.drop_index(op.f("ix_omics_processing_id"), table_name="omics_processing")
+    op.drop_index(op.f("ix_biosample_study_id"), table_name="biosample")
+    op.drop_index(op.f("ix_biosample_id"), table_name="biosample")
+    # ### end Alembic commands ###

nmdc_server/models.py

@@ -210,7 +210,7 @@ class DOIInfo(Base):
 
 
 class AnnotatedModel:
-    id = Column(String, primary_key=True)
+    id = Column(String, primary_key=True, index=True)
     name = Column(String, nullable=False)
     description = Column(String, nullable=False, default="")
 
@@ -312,7 +312,7 @@ class Biosample(Base, AnnotatedModel):
     latitude = Column(Float, nullable=True)
     longitude = Column(Float, nullable=True)
 
-    study_id = Column(String, ForeignKey("study.id"), nullable=False)
+    study_id = Column(String, ForeignKey("study.id"), nullable=False, index=True)
     multiomics = Column(Integer, nullable=False, default=0)
     emsl_biosample_identifiers = Column(JSONB, nullable=True)
     omics_processing = relationship(
@@ -367,7 +367,7 @@ class OmicsProcessing(Base, AnnotatedModel):
     biosample_inputs = relationship(
         "Biosample", secondary=biosample_input_association, back_populates="omics_processing"
     )
-    study_id = Column(String, ForeignKey("study.id"), nullable=True)
+    study_id = Column(String, ForeignKey("study.id"), nullable=True, index=True)
     study = relationship("Study", backref="omics_processing")
 
     outputs = output_relationship(omics_processing_output_association)

nmdc_server/query.py

@@ -896,7 +896,7 @@ class BinnedDateFacetQuery(FacetQuery):
 
 
 class StudySearchResponse(BaseSearchResponse):
-    results: List[schemas.Study]
+    results: List[schemas.StudyBase]
     total: Optional[int]
 
 

nmdc_server/schemas.py

@@ -224,58 +224,61 @@ class Config:
         orm_mode = True
 
 
+class OmicsCounts(BaseModel):
+    type: str
+    count: int
+
+    @validator("count", pre=True, always=True)
+    def insert_zero(cls, v):
+        return v or 0
+
+
 class StudyBase(AnnotatedBase):
-    principal_investigator_websites: Optional[List[str]] = []
-    gold_name: str = ""
-    gold_description: str = ""
-    scientific_objective: str = ""
-    add_date: Optional[DateType]
-    mod_date: Optional[DateType]
-    has_credit_associations: Optional[List[CreditAssociation]]
-    relevant_protocols: Optional[List[str]]
-    funding_sources: Optional[List[str]]
-    gold_study_identifiers: Optional[List[str]]
-    homepage_website: Optional[List[str]]
     part_of: Optional[List[str]]
     study_category: Optional[str]
-    children: Optional[List[Study]] = []
+    children: Optional[List[StudyBase]] = []
+    sample_count: Optional[int]
+    omics_counts: Optional[List[OmicsCounts]]
+    omics_processing_counts: Optional[List[OmicsCounts]]
+    multiomics: int
 
-    @validator("principal_investigator_websites", pre=True, each_item=True)
-    def replace_websites(cls, study_website: Union[models.StudyWebsite, str]) -> str:
-        if isinstance(study_website, str):
-            return study_website
-        return study_website.website.url
+    class Config:
+        orm_mode = True
 
 
 class StudyCreate(StudyBase):
     principal_investigator_id: Optional[UUID]
     image: Optional[bytes]
 
 
-class OmicsCounts(BaseModel):
-    type: str
-    count: int
-
-    @validator("count", pre=True, always=True)
-    def insert_zero(cls, v):
-        return v or 0
-
-
 class Study(StudyBase):
+    principal_investigator_websites: Optional[List[str]] = []
+    gold_name: str = ""
+    gold_description: str = ""
+    scientific_objective: str = ""
+    add_date: Optional[DateType]
+    mod_date: Optional[DateType]
+    has_credit_associations: Optional[List[CreditAssociation]]
+    relevant_protocols: Optional[List[str]]
+    funding_sources: Optional[List[str]]
+    gold_study_identifiers: Optional[List[str]]
+    homepage_website: Optional[List[str]]
     open_in_gold: Optional[str]
     principal_investigator: Optional[OrcidPerson]
     principal_investigator_name: Optional[str]
     image_url: str
     principal_investigator_image_url: str
-    sample_count: Optional[int]
-    omics_counts: Optional[List[OmicsCounts]]
-    omics_processing_counts: Optional[List[OmicsCounts]]
     doi_map: Dict[str, Any] = {}
-    multiomics: int
 
     class Config:
         orm_mode = True
 
+    @validator("principal_investigator_websites", pre=True, each_item=True)
+    def replace_websites(cls, study_website: Union[models.StudyWebsite, str]) -> str:
+        if isinstance(study_website, str):
+            return study_website
+        return study_website.website.url
+
 
 # biosample
 class BiosampleBase(AnnotatedBase):