Fix(Alembic) Remove imports from cg in alembic scripts (#2986)(patch)

### Fixed

- Removed all import from cg in the alembic scripts

alembic/versions/2024_01_25_d241d8c493fb_add_pipeline_to_order.py

@@ -6,10 +6,11 @@
 
 """
 
+from enum import StrEnum
+
 import sqlalchemy as sa
 
 from alembic import op
-from cg.constants import Workflow
 
 # revision identifiers, used by Alembic.
 revision = "d241d8c493fb"
@@ -18,6 +19,25 @@
 depends_on = None
 
 
+class Workflow(StrEnum):
+    BALSAMIC: str = "balsamic"
+    BALSAMIC_QC: str = "balsamic-qc"
+    BALSAMIC_UMI: str = "balsamic-umi"
+    BALSAMIC_PON: str = "balsamic-pon"
+    DEMULTIPLEX: str = "demultiplex"
+    FASTQ: str = "fastq"
+    FLUFFY: str = "fluffy"
+    MICROSALT: str = "microsalt"
+    MIP_DNA: str = "mip-dna"
+    MIP_RNA: str = "mip-rna"
+    RAREDISEASE: str = "raredisease"
+    RNAFUSION: str = "rnafusion"
+    RSYNC: str = "rsync"
+    SARS_COV_2: str = "sars-cov-2"
+    SPRING: str = "spring"
+    TAXPROFILER: str = "taxprofiler"
+
+
 def upgrade():
     op.add_column(
         table_name="order",

alembic/versions/2024_01_25_de0f5b78dca4_rename_pipeline_sars_cov2.py

@@ -6,12 +6,33 @@
 
 """
 
-from sqlalchemy import orm
+from enum import StrEnum
+
+from sqlalchemy import orm, types
 from sqlalchemy.dialects import mysql
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column
 
 from alembic import op
-from cg.constants import Workflow
-from cg.store.models import Analysis, Case
+
+
+class Workflow(StrEnum):
+    BALSAMIC: str = "balsamic"
+    BALSAMIC_PON: str = "balsamic-pon"
+    BALSAMIC_QC: str = "balsamic-qc"
+    BALSAMIC_UMI: str = "balsamic-umi"
+    DEMULTIPLEX: str = "demultiplex"
+    FASTQ: str = "fastq"
+    FLUFFY: str = "fluffy"
+    MICROSALT: str = "microsalt"
+    MIP_DNA: str = "mip-dna"
+    MIP_RNA: str = "mip-rna"
+    MUTANT: str = "mutant"
+    RAREDISEASE: str = "raredisease"
+    RNAFUSION: str = "rnafusion"
+    RSYNC: str = "rsync"
+    SPRING: str = "spring"
+    TAXPROFILER: str = "taxprofiler"
+
 
 # revision identifiers, used by Alembic.
 revision = "de0f5b78dca4"
@@ -44,6 +65,23 @@
 new_enum = mysql.ENUM(*list(new_options))
 
 
+class Base(DeclarativeBase):
+    pass
+
+
+class Analysis(Base):
+    __tablename__ = "analysis"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    pipeline: Mapped[str]
+
+
+class Case(Base):
+    __tablename__ = "case"
+    data_analysis: Mapped[str]
+    id: Mapped[int] = mapped_column(primary_key=True)
+
+
 def upgrade():
     bind = op.get_bind()
     session = orm.Session(bind=bind)

alembic/versions/432379a1adfa_fix_sars_cov_2_data_analysis_to_database.py

@@ -6,13 +6,14 @@
 
 """
 
+from enum import StrEnum
+
 import sqlalchemy as sa
 from sqlalchemy import Column, orm, types
 from sqlalchemy.dialects import mysql
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import DataDelivery, Workflow
 
 Base = declarative_base()
 
@@ -23,13 +24,32 @@
 depends_on = None
 
 
+class DataDelivery(StrEnum):
+    ANALYSIS_FILES: str = "analysis"
+    ANALYSIS_BAM_FILES: str = "analysis-bam"
+    FASTQ: str = "fastq"
+    NIPT_VIEWER: str = "nipt-viewer"
+    FASTQ_QC: str = "fastq_qc"
+    SCOUT: str = "scout"
+
+
+class Pipeline(StrEnum):
+    BALSAMIC: str = "balsamic"
+    FASTQ: str = "fastq"
+    FLUFFY: str = "fluffy"
+    MICROSALT: str = "microsalt"
+    MIP_DNA: str = "mip-dna"
+    MIP_RNA: str = "mip-rna"
+    SARS_COV_2: str = "sars-cov-2"
+
+
 class Case(Base):
     __tablename__ = "family"
 
     id = sa.Column(sa.types.Integer, primary_key=True)
     internal_id = sa.Column(sa.types.String(32), unique=True, nullable=False)
     name = sa.Column(sa.types.String(128), nullable=False)
-    data_analysis = Column(types.Enum(*list(Workflow)))
+    data_analysis = Column(types.Enum(*list(Pipeline)))
     data_delivery = Column(types.Enum(*list(DataDelivery)))
 
     def __str__(self) -> str:
@@ -58,7 +78,7 @@ def upgrade():
         .filter(Case.data_analysis == "")
     ):
         print(f"Altering family: {str(family)}")
-        family.data_analysis = str(Workflow.SARS_COV_2)
+        family.data_analysis = str(Pipeline.SARS_COV_2)
         print(f"Altered family: {str(family)}")
 
     session.commit()

alembic/versions/68e54d17f4f3_add_is_clinical_to_customer.py

@@ -7,9 +7,10 @@
 """
 
 import sqlalchemy as sa
+from sqlalchemy import Column, types
+from sqlalchemy.orm import DeclarativeBase
 
 from alembic import op
-from cg.store.models import Customer
 
 # revision identifiers, used by Alembic.
 revision = "68e54d17f4f3"
@@ -18,6 +19,16 @@
 depends_on = None
 
 
+class Model(DeclarativeBase):
+    pass
+
+
+class Customer(Model):
+    __tablename__ = "customer"
+    id = Column(types.Integer, primary_key=True)
+    is_clinical = Column(types.Boolean, nullable=True)
+
+
 def upgrade():
     op.add_column(table_name="customer", column=sa.Column("is_clinical", sa.BOOLEAN))
     bind = op.get_bind()

alembic/versions/9008aa5065b4_add_taxprofiler_analysis_option.py

@@ -6,12 +6,13 @@
 
 """
 
+from enum import StrEnum
+
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import Workflow
 
 # revision identifiers, used by Alembic.
 revision = "9008aa5065b4"
@@ -43,6 +44,25 @@
 new_enum = mysql.ENUM(*new_options)
 
 
+class Workflow(StrEnum):
+    BALSAMIC: str = "balsamic"
+    BALSAMIC_PON: str = "balsamic-pon"
+    BALSAMIC_QC: str = "balsamic-qc"
+    BALSAMIC_UMI: str = "balsamic-umi"
+    DEMULTIPLEX: str = "demultiplex"
+    FASTQ: str = "fastq"
+    FLUFFY: str = "fluffy"
+    MICROSALT: str = "microsalt"
+    MIP_DNA: str = "mip-dna"
+    MIP_RNA: str = "mip-rna"
+    MUTANT: str = "mutant"
+    RAREDISEASE: str = "raredisease"
+    RNAFUSION: str = "rnafusion"
+    RSYNC: str = "rsync"
+    SPRING: str = "spring"
+    TAXPROFILER: str = "taxprofiler"
+
+
 class Analysis(Base):
     __tablename__ = "analysis"
     id = sa.Column(sa.types.Integer, primary_key=True)

alembic/versions/9073c61bc72b_add_raredisease_to_analysis_options.py

@@ -6,12 +6,13 @@
 
 """
 
+from enum import StrEnum
+
 import sqlalchemy as sa
 from sqlalchemy.dialects import mysql
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import Workflow
 
 # revision identifiers, used by Alembic.
 revision = "9073c61bc72b"
@@ -38,6 +39,27 @@
     "spring",
     "taxprofiler",
 )
+
+
+class Pipeline(StrEnum):
+    BALSAMIC: str = "balsamic"
+    BALSAMIC_QC: str = "balsamic-qc"
+    BALSAMIC_UMI: str = "balsamic-umi"
+    BALSAMIC_PON: str = "balsamic-pon"
+    DEMULTIPLEX: str = "demultiplex"
+    FASTQ: str = "fastq"
+    FLUFFY: str = "fluffy"
+    MICROSALT: str = "microsalt"
+    MIP_DNA: str = "mip-dna"
+    MIP_RNA: str = "mip-rna"
+    RAREDISEASE: str = "raredisease"
+    RNAFUSION: str = "rnafusion"
+    RSYNC: str = "rsync"
+    SARS_COV_2: str = "sars-cov-2"
+    SPRING: str = "spring"
+    TAXPROFILER: str = "taxprofiler"
+
+
 new_analysis_options = sorted(old_analysis_options + ("raredisease",))
 
 old_analysis_enum = mysql.ENUM(*old_analysis_options)
@@ -47,13 +69,14 @@
 class Analysis(Base):
     __tablename__ = "analysis"
     id = sa.Column(sa.types.Integer, primary_key=True)
-    pipeline = sa.Column(sa.types.Enum(*list(Workflow)))
+    pipeline = sa.Column(sa.types.Enum(*list(Pipeline)))
 
 
 class Case(Base):
     __tablename__ = "family"
     id = sa.Column(sa.types.Integer, primary_key=True)
-    data_analysis = sa.Column(sa.types.Enum(*list(Workflow)))
+    data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
+    internal_id = sa.Column(sa.types.String)
 
 
 def upgrade():

alembic/versions/998be2e367cf_fix_mip_on_fastq_wgs_cases.py

@@ -7,13 +7,13 @@
 """
 
 from datetime import datetime
+from enum import StrEnum
 
 import sqlalchemy as sa
 from sqlalchemy import orm
 from sqlalchemy.orm import declarative_base
 
 from alembic import op
-from cg.constants import PREP_CATEGORIES, DataDelivery, Workflow
 
 Base = declarative_base()
 
@@ -23,6 +23,27 @@
 branch_labels = None
 depends_on = None
 
+PREP_CATEGORIES = ("cov", "mic", "rml", "tgs", "wes", "wgs", "wts")
+
+
+class DataDelivery(StrEnum):
+    ANALYSIS_FILES: str = "analysis"
+    ANALYSIS_BAM_FILES: str = "analysis-bam"
+    FASTQ: str = "fastq"
+    NIPT_VIEWER: str = "nipt-viewer"
+    FASTQ_QC: str = "fastq_qc"
+    SCOUT: str = "scout"
+
+
+class Pipeline(StrEnum):
+    BALSAMIC: str = "balsamic"
+    FASTQ: str = "fastq"
+    FLUFFY: str = "fluffy"
+    MICROSALT: str = "microsalt"
+    MIP_DNA: str = "mip-dna"
+    MIP_RNA: str = "mip-rna"
+    SARS_COV_2: str = "sars-cov-2"
+
 
 class Customer(Base):
     __tablename__ = "customer"
@@ -38,7 +59,7 @@ class Case(Base):
     name = sa.Column(sa.types.String(128), nullable=False)
     customer_id = sa.Column(sa.ForeignKey("customer.id", ondelete="CASCADE"), nullable=False)
     customer = orm.relationship(Customer, foreign_keys=[customer_id])
-    data_analysis = sa.Column(sa.types.Enum(*list(Workflow)))
+    data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
     data_delivery = sa.Column(sa.types.Enum(*list(DataDelivery)))
     priority = sa.Column(sa.types.Integer, default=1, nullable=False)
     _panels = sa.Column(sa.types.Text)
@@ -111,7 +132,7 @@ def upgrade():
         session.query(Case)
         .filter(Case.customer_id == 1)
         .filter(Case.data_delivery == DataDelivery.FASTQ)
-        .filter(Case.data_analysis == Workflow.FASTQ)
+        .filter(Case.data_analysis == Pipeline.FASTQ)
         .filter(Case.priority == "research")
         .filter(Case.ordered_at >= datetime(year=2021, month=2, day=2))
     ):
@@ -126,7 +147,7 @@ def upgrade():
                 and sample.name == family.name
             ):
                 print(f"changing data analysis from FASTQ to MIP for: {family}")
-                family.data_analysis = Workflow.MIP_DNA
+                family.data_analysis = Pipeline.MIP_DNA
                 count += 1
 
     session.commit()
@@ -143,7 +164,7 @@ def downgrade():
         session.query(Case)
         .filter(Case.customer_id == 1)
         .filter(Case.data_delivery == DataDelivery.FASTQ)
-        .filter(Case.data_analysis == Workflow.MIP_DNA)
+        .filter(Case.data_analysis == Pipeline.MIP_DNA)
         .filter(Case.priority == "research")
         .filter(Case.ordered_at >= datetime(year=2021, month=2, day=2))
     ):
@@ -158,7 +179,7 @@ def downgrade():
                 and sample.name == family.name
             ):
                 print(f"changing data analysis from MIP to FASTQ for: {family}")
-                family.data_analysis = Workflow.FASTQ
+                family.data_analysis = Pipeline.FASTQ
                 count += 1
 
     session.commit()