WIP #97, WIP tests fail

Author: eboileau

Diff for: server/migrations/versions/80658585dbb2_add_trna.py

@@ -0,0 +1,58 @@
+"""add_trna
+
+Revision ID: 80658585dbb2
+Revises: 622810482837
+Create Date: 2024-06-11 14:25:58.871272
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "80658585dbb2"
+down_revision = "622810482837"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "sprinzl",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("data_id", sa.Integer(), nullable=False),
+        sa.Column("position", sa.String(length=32), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["data_id"], ["data.id"], name=op.f("fk_sprinzl_data_id_data")
+        ),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_sprinzl")),
+        sa.UniqueConstraint("data_id", "position", name=op.f("uq_sprinzl_data_id")),
+    )
+    op.create_index(op.f("ix_sprinzl_data_id"), "sprinzl", ["data_id"], unique=False)
+    op.add_column(
+        "annotation", sa.Column("source", sa.String(length=128), nullable=False)
+    )
+    op.drop_constraint("uq_annotation_rtv", "annotation", type_="unique")
+    op.create_unique_constraint(
+        "uq_annotation_rtv", "annotation", ["release", "taxa_id", "source", "version"]
+    )
+    op.add_column(
+        "assembly", sa.Column("alt_name", sa.String(length=128), nullable=False)
+    )
+    op.create_unique_constraint(op.f("uq_assembly_alt_name"), "assembly", ["alt_name"])
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint(op.f("uq_assembly_alt_name"), "assembly", type_="unique")
+    op.drop_column("assembly", "alt_name")
+    op.drop_constraint("uq_annotation_rtv", "annotation", type_="unique")
+    op.create_unique_constraint(
+        "uq_annotation_rtv", "annotation", ["release", "taxa_id", "version"]
+    )
+    op.drop_column("annotation", "source")
+    op.drop_index(op.f("ix_sprinzl_data_id"), table_name="sprinzl")
+    op.drop_table("sprinzl")
+    # ### end Alembic commands ###

Diff for: server/migrations/versions/be4f58630610_assembly_drop_constraint.py

@@ -0,0 +1,34 @@
+"""assembly_drop_constraint
+
+Revision ID: be4f58630610
+Revises: 80658585dbb2
+Create Date: 2024-06-11 17:16:15.019905
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import mysql
+
+# revision identifiers, used by Alembic.
+revision = "be4f58630610"
+down_revision = "80658585dbb2"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "assembly", "alt_name", existing_type=mysql.VARCHAR(length=128), nullable=True
+    )
+    op.drop_index("uq_assembly_alt_name", table_name="assembly")
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_index("uq_assembly_alt_name", "assembly", ["alt_name"], unique=True)
+    op.alter_column(
+        "assembly", "alt_name", existing_type=mysql.VARCHAR(length=128), nullable=False
+    )
+    # ### end Alembic commands ###

Diff for: server/src/scimodom/database/models.py

@@ -190,6 +190,7 @@ class Assembly(Base):
 
     id: Mapped[int] = mapped_column(primary_key=True)
     name: Mapped[str] = mapped_column(String(128), nullable=False, unique=True)
+    alt_name: Mapped[str] = mapped_column(String(128), nullable=True)
     taxa_id: Mapped[int] = mapped_column(ForeignKey("ncbi_taxa.id"), index=True)
     version: Mapped[str] = mapped_column(
         String(12), nullable=False
@@ -216,12 +217,13 @@ class Annotation(Base):
     id: Mapped[int] = mapped_column(primary_key=True)
     release: Mapped[int] = mapped_column(nullable=False)
     taxa_id: Mapped[int] = mapped_column(ForeignKey("ncbi_taxa.id"), index=True)
+    source: Mapped[str] = mapped_column(String(128), nullable=False)
     version: Mapped[str] = mapped_column(
         String(12), nullable=False
     )  # current is annotation_version.version_num
 
     __table_args__ = (
-        UniqueConstraint(release, taxa_id, version, name="uq_annotation_rtv"),
+        UniqueConstraint(release, taxa_id, source, version, name="uq_annotation_rtv"),
     )
 
     inst_taxa: Mapped["Taxa"] = relationship(back_populates="annotations")
@@ -245,12 +247,14 @@ class GenomicAnnotation(Base):
 
     id: Mapped[str] = mapped_column(
         String(128), primary_key=True, autoincrement=False
-    )  # Ensembl ID
+    )  # Ensembl ID or GtRNAdb_id incl. organism
     annotation_id: Mapped[int] = mapped_column(ForeignKey("annotation.id"), index=True)
-    name: Mapped[str] = mapped_column(String(128), nullable=True)  # Ensembl gene name
+    name: Mapped[str] = mapped_column(
+        String(128), nullable=True
+    )  # Ensembl gene name or GtRNAdb_id
     biotype: Mapped[str] = mapped_column(
         String(255), nullable=True
-    )  # Ensembl gene biotype
+    )  # Ensembl gene biotype or tRNA
 
     __table_args__ = (Index("idx_genomic", "annotation_id", "biotype", "name"),)
 
@@ -437,6 +441,18 @@ class DataAnnotation(Base):
     inst_data: Mapped["Data"] = relationship(back_populates="annotations")
 
 
+class Sprinzl(Base):
+    """Sprinzl tRNA position numbering"""
+
+    __tablename__ = "sprinzl"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    data_id: Mapped[int] = mapped_column(ForeignKey("data.id"), index=True)
+    position: Mapped[str] = mapped_column(String(32), nullable=False)
+
+    __table_args__ = (UniqueConstraint(data_id, position),)
+
+
 class UserState(enum.Enum):
     wait_for_confirmation = 0
     active = 1