Rename Family to Case (#2655)(patch)

alembic/versions/20750539a335_add_ticket_to_families.py

@@ -23,7 +23,7 @@
 Base = declarative_base()
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
 
     id = sa.Column(sa.types.Integer, primary_key=True)
@@ -37,7 +37,7 @@ class FamilySample(Base):
     family_id = sa.Column(sa.ForeignKey("family.id", ondelete="CASCADE"), nullable=False)
     sample_id = sa.Column(sa.ForeignKey("sample.id", ondelete="CASCADE"), nullable=False)
 
-    family = sa.orm.relationship("Family", backref="links")
+    family = sa.orm.relationship("Case", backref="links")
     sample = sa.orm.relationship("Sample", foreign_keys=[sample_id], backref="links")
 
 
@@ -60,7 +60,7 @@ def upgrade():
     op.add_column("family", sa.Column("tickets", type_=mysql.VARCHAR(128), nullable=True))
     bind = op.get_bind()
     session = sa.orm.Session(bind=bind)
-    for family in session.query(Family):
+    for family in session.query(Case):
         if len(family.links) == 0:
             continue
         family.tickets = sorted(

alembic/versions/2968d39ac35f_changes_in_delivery_options.py

@@ -53,7 +53,7 @@
 }
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
     id = Column(types.Integer, primary_key=True)
     data_delivery = Column(types.VARCHAR(64))
@@ -64,7 +64,7 @@ def upgrade():
     op.alter_column("family", "data_delivery", type_=types.VARCHAR(64))
     bind = op.get_bind()
     session = sa.orm.Session(bind=bind)
-    for case in session.query(Family):
+    for case in session.query(Case):
         if case.data_delivery in removed_options:
             case.data_delivery = update_map[case.data_delivery]
 
@@ -74,7 +74,7 @@ def upgrade():
 def downgrade():
     bind = op.get_bind()
     session = sa.orm.Session(bind=bind)
-    for case in session.query(Family):
+    for case in session.query(Case):
         if case.data_delivery == "":
             case.data_delivery = None
         if case.data_delivery in added_options:

alembic/versions/432379a1adfa_fix_sars_cov_2_data_analysis_to_database.py

@@ -22,7 +22,7 @@
 depends_on = None
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
 
     id = sa.Column(sa.types.Integer, primary_key=True)
@@ -52,9 +52,9 @@ def upgrade():
     op.alter_column("analysis", "pipeline", type_=new_enum)
 
     for family in (
-        session.query(Family)
-        .filter(Family.data_delivery == str(DataDelivery.FASTQ))
-        .filter(Family.data_analysis == "")
+        session.query(Case)
+        .filter(Case.data_delivery == str(DataDelivery.FASTQ))
+        .filter(Case.data_analysis == "")
     ):
         print(f"Altering family: {str(family)}")
         family.data_analysis = str(Pipeline.SARS_COV_2)

alembic/versions/7e344b9438bf_petname_avatar.py

@@ -22,7 +22,7 @@
 Base = declarative_base()
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
 
     id = sa.Column(sa.types.Integer, primary_key=True)
@@ -36,7 +36,7 @@ def __str__(self) -> str:
 
 
 def find_family_by_avatar_url(avatar_url, session):
-    return session.query(Family).filter_by(avatar_url=avatar_url).first()
+    return session.query(Case).filter_by(avatar_url=avatar_url).first()
 
 
 def upgrade():

alembic/versions/9008aa5065b4_add_taxprofiler_analysis_option.py

@@ -48,7 +48,7 @@ class Analysis(Base):
     pipeline = sa.Column(sa.types.Enum(*list(Pipeline)))
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
     id = sa.Column(sa.types.Integer, primary_key=True)
     data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
@@ -64,6 +64,6 @@ def downgrade():
     session = sa.orm.Session(bind=bind)
     for analysis in session.query(Analysis).filter(Analysis.pipeline == "taxprofiler"):
         analysis.pipeline = "fastq"
-    for family in session.query(Family).filter(Family.data_analysis == "taxprofiler"):
+    for family in session.query(Case).filter(Case.data_analysis == "taxprofiler"):
         family.data_analysis = "fastq"
     session.commit()

alembic/versions/9073c61bc72b_add_raredisease_to_analysis_options.py

@@ -49,7 +49,7 @@ class Analysis(Base):
     pipeline = sa.Column(sa.types.Enum(*list(Pipeline)))
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
     id = sa.Column(sa.types.Integer, primary_key=True)
     data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
@@ -68,8 +68,8 @@ def downgrade():
             f"Changing pipeline for Analysis {Analysis.family.internal_id}, {Analysis.completed_at} to mip-dna"
         )
         analysis.pipeline = "mip-dna"
-    for family in session.query(Family).filter(Family.data_analysis == "raredisease"):
-        print(f"Changing data_analysis for Family {family.internal_id} to mip-dna")
+    for family in session.query(Case).filter(Case.data_analysis == "raredisease"):
+        print(f"Changing data_analysis for Case {family.internal_id} to mip-dna")
         family.data_analysis = "mip-dna"
     op.alter_column("family", "data_analysis", type_=old_analysis_enum)
     op.alter_column("analysis", "pipeline", type_=old_analysis_enum)

alembic/versions/998be2e367cf_fix_mip_on_fastq_wgs_cases.py

@@ -29,7 +29,7 @@ class Customer(Base):
     id = sa.Column(sa.types.Integer, primary_key=True)
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
 
     id = sa.Column(sa.types.Integer, primary_key=True)
@@ -63,7 +63,7 @@ class FamilySample(Base):
     mother_id = sa.Column(sa.ForeignKey("sample.id"))
     father_id = sa.Column(sa.ForeignKey("sample.id"))
 
-    family = orm.relationship("Family", backref="links")
+    family = orm.relationship("Case", backref="links")
     sample = orm.relationship("Sample", foreign_keys=[sample_id], backref="links")
     mother = orm.relationship("Sample", foreign_keys=[mother_id], backref="mother_links")
     father = orm.relationship("Sample", foreign_keys=[father_id], backref="father_links")
@@ -107,12 +107,12 @@ def upgrade():
     count = 0
     # change records that should have been run with MIP for MAF
     for family in (
-        session.query(Family)
-        .filter(Family.customer_id == 1)
-        .filter(Family.data_delivery == DataDelivery.FASTQ)
-        .filter(Family.data_analysis == Pipeline.FASTQ)
-        .filter(Family.priority == "research")
-        .filter(Family.ordered_at >= datetime(year=2021, month=2, day=2))
+        session.query(Case)
+        .filter(Case.customer_id == 1)
+        .filter(Case.data_delivery == DataDelivery.FASTQ)
+        .filter(Case.data_analysis == Pipeline.FASTQ)
+        .filter(Case.priority == "research")
+        .filter(Case.ordered_at >= datetime(year=2021, month=2, day=2))
     ):
         if len(family.links) > 1:
             print(f"skipping case that has more than one link: {family}")
@@ -139,12 +139,12 @@ def downgrade():
 
     count = 0
     for family in (
-        session.query(Family)
-        .filter(Family.customer_id == 1)
-        .filter(Family.data_delivery == DataDelivery.FASTQ)
-        .filter(Family.data_analysis == Pipeline.MIP_DNA)
-        .filter(Family.priority == "research")
-        .filter(Family.ordered_at >= datetime(year=2021, month=2, day=2))
+        session.query(Case)
+        .filter(Case.customer_id == 1)
+        .filter(Case.data_delivery == DataDelivery.FASTQ)
+        .filter(Case.data_analysis == Pipeline.MIP_DNA)
+        .filter(Case.priority == "research")
+        .filter(Case.ordered_at >= datetime(year=2021, month=2, day=2))
     ):
         if len(family.links) > 1:
             print(f"skipping case that has more than one link: {family}")

alembic/versions/e9df15a35de4_fix_tumour_not_to_maf.py

@@ -29,7 +29,7 @@ class Customer(Base):
     id = sa.Column(sa.types.Integer, primary_key=True)
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
 
     id = sa.Column(sa.types.Integer, primary_key=True)
@@ -63,7 +63,7 @@ class FamilySample(Base):
     mother_id = sa.Column(sa.ForeignKey("sample.id"))
     father_id = sa.Column(sa.ForeignKey("sample.id"))
 
-    family = orm.relationship("Family", backref="links")
+    family = orm.relationship("Case", backref="links")
     sample = orm.relationship("Sample", foreign_keys=[sample_id], backref="links")
     mother = orm.relationship("Sample", foreign_keys=[mother_id], backref="mother_links")
     father = orm.relationship("Sample", foreign_keys=[father_id], backref="father_links")
@@ -108,11 +108,11 @@ def upgrade():
     count = 0
     # change records that should is tumour and should not be sent to MAF
     for family in (
-        session.query(Family)
-        .filter(Family.customer_id == 1)
-        .filter(Family.data_delivery == DataDelivery.FASTQ)
-        .filter(Family.data_analysis == Pipeline.MIP_DNA)
-        .filter(Family.priority == "research")
+        session.query(Case)
+        .filter(Case.customer_id == 1)
+        .filter(Case.data_delivery == DataDelivery.FASTQ)
+        .filter(Case.data_analysis == Pipeline.MIP_DNA)
+        .filter(Case.priority == "research")
     ):
         if len(family.links) > 1:
             print(f"skipping case that has more than one link: {family}")
@@ -142,11 +142,11 @@ def downgrade():
 
     count = 0
     for family in (
-        session.query(Family)
-        .filter(Family.customer_id == 1)
-        .filter(Family.data_delivery == DataDelivery.FASTQ)
-        .filter(Family.data_analysis == Pipeline.FASTQ)
-        .filter(Family.priority == "research")
+        session.query(Case)
+        .filter(Case.customer_id == 1)
+        .filter(Case.data_delivery == DataDelivery.FASTQ)
+        .filter(Case.data_analysis == Pipeline.FASTQ)
+        .filter(Case.priority == "research")
     ):
         if len(family.links) > 1:
             print(f"skipping case that has more than one link: {family}")

alembic/versions/fab30255b84f_move_synopsis_to_case.py

@@ -22,7 +22,7 @@
 depends_on = None
 
 
-class Family(Base):
+class Case(Base):
     __tablename__ = "family"
 
     id = sa.Column(sa.types.Integer, primary_key=True)
@@ -62,7 +62,7 @@ class FamilySample(Base):
     mother_id = sa.Column(sa.ForeignKey("sample.id"))
     father_id = sa.Column(sa.ForeignKey("sample.id"))
 
-    family = orm.relationship("Family", backref="links")
+    family = orm.relationship("Case", backref="links")
     sample = orm.relationship("Sample", foreign_keys=[sample_id], backref="links")
     mother = orm.relationship("Sample", foreign_keys=[mother_id], backref="mother_links")
     father = orm.relationship("Sample", foreign_keys=[father_id], backref="father_links")
@@ -122,10 +122,10 @@ def downgrade():
     op.add_column("sample", sa.Column("_cohorts", sa.TEXT))
 
     # copy data from family._synopsis to sample._synopsis
-    for family in session.query(Family).filter(Family._synopsis.isnot(None)):
+    for family in session.query(Case).filter(Case._synopsis.isnot(None)):
         for link in family.links:
             link.sample._synopsis = family._synopsis
-    for family in session.query(Family).filter(Family._cohorts.isnot(None)):
+    for family in session.query(Case).filter(Case._cohorts.isnot(None)):
         for link in family.links:
             link.sample._cohorts = family._cohorts
     session.commit()

cg/apps/downsample/downsample.py

@@ -8,7 +8,7 @@
 from cg.meta.workflow.downsample.downsample import DownsampleWorkflow
 from cg.models.cg_config import CGConfig
 from cg.models.downsample.downsample_data import DownsampleData
-from cg.store.models import Family, FamilySample, Sample
+from cg.store.models import Case, FamilySample, Sample
 from cg.utils.calculations import multiply_by_million
 
 LOG = logging.getLogger(__name__)
@@ -67,7 +67,7 @@ def store_downsampled_case(self, downsample_data: DownsampleData) -> None:
         """
         Add a down sampled case entry to StatusDB.
         """
-        downsampled_case: Family = downsample_data.downsampled_case
+        downsampled_case: Case = downsample_data.downsampled_case
         if self.status_db.case_with_name_exists(case_name=downsampled_case.name):
             LOG.info(f"Case with name {downsampled_case.name} already exists in StatusDB.")
             return
@@ -77,7 +77,7 @@ def store_downsampled_case(self, downsample_data: DownsampleData) -> None:
             LOG.info(f"New down sampled case created: {downsampled_case.internal_id}")
 
     def _link_downsampled_sample_to_case(
-        self, downsample_data: DownsampleData, sample: Sample, case: Family
+        self, downsample_data: DownsampleData, sample: Sample, case: Case
     ) -> None:
         """Create a link between sample and case in statusDB."""
         sample_case_link: FamilySample = self.status_db.relate_sample(

cg/cli/add.py

@@ -13,7 +13,7 @@
     ApplicationVersion,
     Collaboration,
     Customer,
-    Family,
+    Case,
     FamilySample,
     Panel,
     Sample,
@@ -264,7 +264,7 @@ def add_case(
             LOG.error(f"{panel_abbreviation}: panel not found")
             raise click.Abort
 
-    new_case: Family = status_db.add_case(
+    new_case: Case = status_db.add_case(
         data_analysis=data_analysis,
         data_delivery=data_delivery,
         name=name,
@@ -298,7 +298,7 @@ def link_sample_to_case(
     status_db: Store = context.status_db
     mother: Optional[Sample] = None
     father: Optional[Sample] = None
-    case_obj: Family = status_db.get_case_by_internal_id(internal_id=case_id)
+    case_obj: Case = status_db.get_case_by_internal_id(internal_id=case_id)
     if case_obj is None:
         LOG.error("%s: family not found", case_id)
         raise click.Abort

cg/cli/compress/fastq.py

@@ -17,7 +17,7 @@
 from cg.meta.compress import CompressAPI
 from cg.models.cg_config import CGConfig
 from cg.store import Store
-from cg.store.models import Family, Sample
+from cg.store.models import Case, Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -51,7 +51,7 @@ def fastq_cmd(
     LOG.info("Running compress FASTQ")
     compress_api: CompressAPI = context.meta_apis["compress_api"]
     store: Store = context.status_db
-    cases: list[Family] = get_cases_to_process(case_id=case_id, days_back=days_back, store=store)
+    cases: list[Case] = get_cases_to_process(case_id=case_id, days_back=days_back, store=store)
     if not cases:
         LOG.info("No cases to compress")
         return None
@@ -84,7 +84,7 @@ def clean_fastq(context: CGConfig, case_id: Optional[str], days_back: int, dry_r
     store: Store = context.status_db
     update_compress_api(compress_api, dry_run=dry_run)
 
-    cases: list[Family] = get_cases_to_process(case_id=case_id, days_back=days_back, store=store)
+    cases: list[Case] = get_cases_to_process(case_id=case_id, days_back=days_back, store=store)
     if not cases:
         return
 

cg/cli/compress/helpers.py

@@ -15,27 +15,25 @@
 from cg.meta.compress import CompressAPI
 from cg.meta.compress.files import get_spring_paths
 from cg.store import Store
-from cg.store.models import Family
+from cg.store.models import Case
 from cg.utils.date import get_date_days_ago
 
 LOG = logging.getLogger(__name__)
 
 
-def get_cases_to_process(
-    days_back: int, store: Store, case_id: Optional[str] = None
-) -> Optional[list[Family]]:
+def get_cases_to_process(days_back: int, store: Store, case_id: Optional[str] = None) -> list[Case]:
     """Return cases to process."""
-    cases: list[Family] = []
+    cases: list[Case] = []
     if case_id:
-        case: Family = store.get_case_by_internal_id(case_id)
+        case: Case = store.get_case_by_internal_id(case_id)
         if not case:
             LOG.warning(f"Could not find case {case_id}")
             return
         if case.is_compressible:
             cases.append(case)
     else:
         date_threshold: dt.datetime = get_date_days_ago(days_ago=days_back)
-        cases: list[Family] = store.get_cases_to_compress(date_threshold=date_threshold)
+        cases: list[Case] = store.get_cases_to_compress(date_threshold=date_threshold)
     return cases
 
 
@@ -125,7 +123,7 @@ def get_true_dir(dir_path: Path) -> Optional[Path]:
 
 def compress_sample_fastqs_in_cases(
     compress_api: CompressAPI,
-    cases: list[Family],
+    cases: list[Case],
     dry_run: bool,
     number_of_conversions: int,
     hours: int = None,