add Raredisease order type to database

alembic/versions/2025_04_28_039dbdf8af01_add_raredisease_ordertype.py

@@ -0,0 +1,104 @@
+"""add Raredisease ordertype
+
+Revision ID: 039dbdf8af01
+Revises: 6362cfd4c61f
+Create Date: 2025-04-25 13:57:47.960893
+
+"""
+
+from enum import StrEnum
+
+import sqlalchemy as sa
+from sqlalchemy.orm import declarative_base
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "039dbdf8af01"
+down_revision = "6362cfd4c61f"
+branch_labels = None
+depends_on = None
+
+Base = declarative_base()
+
+
+class OrderType(StrEnum):
+    BALSAMIC = "balsamic"
+    BALSAMIC_UMI = "balsamic-umi"
+    FASTQ = "fastq"
+    FLUFFY = "fluffy"
+    METAGENOME = "metagenome"
+    MICROBIAL_FASTQ = "microbial-fastq"
+    MICROSALT = "microsalt"
+    MIP_DNA = "mip-dna"
+    MIP_RNA = "mip-rna"
+    NALLO = "nallo"
+    PACBIO_LONG_READ = "pacbio-long-read"
+    RML = "rml"
+    RNAFUSION = "rnafusion"
+    SARS_COV_2 = "sars-cov-2"
+    TAXPROFILER = "taxprofiler"
+    TOMTE = "tomte"
+
+
+old_order_types = [
+    "BALSAMIC",
+    "BALSAMIC_UMI",
+    "FASTQ",
+    "FLUFFY",
+    "METAGENOME",
+    "MICROBIAL_FASTQ",
+    "MICROSALT",
+    "MIP_DNA",
+    "MIP_RNA",
+    "PACBIO_LONG_READ",
+    "NALLO",
+    "RML",
+    "RNAFUSION",
+    "SARS_COV_2",
+    "TAXPROFILER",
+    "TOMTE",
+]
+
+new_order_types = old_order_types.copy()
+new_order_types.append("RAREDISEASE")
+new_order_types.sort()
+
+
+class OrderTypeApplication(Base):
+    """Maps an order type to its allowed applications"""
+
+    __tablename__ = "order_type_application"
+    order_type = sa.Column(sa.types.Enum(*list(OrderType)), primary_key=True)
+
+
+def upgrade():
+    op.alter_column(
+        table_name="order_type_application",
+        column_name="order_type",
+        existing_type=sa.Enum(*old_order_types),
+        type_=sa.Enum(*new_order_types),
+        nullable=False,
+    )
+
+
+def downgrade():
+    # Remove incompatible entries
+    bind = op.get_bind()
+    session = sa.orm.Session(bind=bind)
+
+    for link in session.query(OrderTypeApplication).filter(
+        OrderTypeApplication.order_type == "RAREDISEASE"
+    ):
+        session.delete(link)
+
+    session.commit()
+
+    # Modify the column type back to the old enum
+    op.alter_column(
+        table_name="order_type_application",
+        column_name="order_type",
+        existing_type=sa.Enum(*new_order_types),
+        type_=sa.Enum(*old_order_types),
+        nullable=False,
+    )

cg/models/orders/constants.py

@@ -4,22 +4,23 @@
 
 
 class OrderType(StrEnum):
-    BALSAMIC: str = Workflow.BALSAMIC
-    BALSAMIC_UMI: str = Workflow.BALSAMIC_UMI
-    FASTQ: str = "fastq"
-    FLUFFY: str = Workflow.FLUFFY
-    METAGENOME: str = "metagenome"
-    MICROBIAL_FASTQ: str = "microbial-fastq"
-    MICROSALT: str = Workflow.MICROSALT
-    MIP_DNA: str = Workflow.MIP_DNA
-    MIP_RNA: str = Workflow.MIP_RNA
+    BALSAMIC = Workflow.BALSAMIC
+    BALSAMIC_UMI = Workflow.BALSAMIC_UMI
+    FASTQ = "fastq"
+    FLUFFY = Workflow.FLUFFY
+    METAGENOME = "metagenome"
+    MICROBIAL_FASTQ = "microbial-fastq"
+    MICROSALT = Workflow.MICROSALT
+    MIP_DNA = Workflow.MIP_DNA
+    MIP_RNA = Workflow.MIP_RNA
     NALLO = Workflow.NALLO
     PACBIO_LONG_READ = "pacbio-long-read"
-    RML: str = "rml"
-    RNAFUSION: str = Workflow.RNAFUSION
-    SARS_COV_2: str = "sars-cov-2"
-    TAXPROFILER: str = Workflow.TAXPROFILER
-    TOMTE: str = Workflow.TOMTE
+    RML = "rml"
+    RAREDISEASE = Workflow.RAREDISEASE
+    RNAFUSION = Workflow.RNAFUSION
+    SARS_COV_2 = "sars-cov-2"
+    TAXPROFILER = Workflow.TAXPROFILER
+    TOMTE = Workflow.TOMTE
 
 
 class ExcelSampleAliases(StrEnum):