Merge branch 'master' into refactor-enums-sex-phenotypestatus

# Conflicts:
#	cg/cli/add.py
#	tests/conftest.py

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 60.7.18
+current_version = 60.8.7
 commit = True
 tag = True
 tag_name = v{new_version}

.github/workflows/tests_and_coverage.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   tests-coverage:
-    runs-on: ubuntu-latest
+    runs-on: 8_core_linux
 
     steps:
       - name: Checkout Repository
@@ -37,7 +37,7 @@ jobs:
 
       - name: Test with pytest & Coveralls
         run: |
-          pytest -n auto --cov=cg/
+          pytest -n logical --cov=cg/
           coveralls
         env:
           COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}

alembic/versions/2024_05_16_6e6c36d5157b_add_illumina_run_metrics.py

@@ -0,0 +1,52 @@
+"""add_illumina_run_metrics
+
+Revision ID: 6e6c36d5157b
+Revises: 5c6de08c4aca
+Create Date: 2024-05-16 13:40:36.754552
+
+"""
+
+from enum import StrEnum
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "6e6c36d5157b"
+down_revision = "5c6de08c4aca"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.create_table(
+        "illumina_sequencing_metrics",
+        sa.Column(
+            "id", sa.Integer(), sa.ForeignKey("run_metrics.id"), nullable=False, primary_key=True
+        ),
+        sa.Column("sequencer_type", sa.String(length=32), nullable=True),
+        sa.Column("sequencer_name", sa.String(length=32), nullable=True),
+        sa.Column("sequenced_at", sa.DateTime(), nullable=True),
+        sa.Column("data_availability", sa.String(length=32), nullable=True),
+        sa.Column("archived_at", sa.DateTime(), nullable=True),
+        sa.Column("has_backup", sa.Boolean(), nullable=False),
+        sa.Column("total_reads", sa.BigInteger(), nullable=True),
+        sa.Column("total_undetermined_reads", sa.BigInteger(), nullable=True),
+        sa.Column("percent_q30", sa.Numeric(precision=6, scale=2), nullable=True),
+        sa.Column("mean_quality_score", sa.Numeric(precision=6, scale=2), nullable=True),
+        sa.Column("total_yield", sa.BigInteger(), nullable=True),
+        sa.Column("yield_q30", sa.Numeric(precision=6, scale=2), nullable=True),
+        sa.Column("cycles", sa.Integer(), nullable=True),
+        sa.Column("demultiplexing_software", sa.String(length=32), nullable=True),
+        sa.Column("demultiplexing_software_version", sa.String(length=32), nullable=True),
+        sa.Column("sequencing_started_at", sa.DateTime(), nullable=True),
+        sa.Column("sequencing_completed_at", sa.DateTime(), nullable=True),
+        sa.Column("demultiplexing_started_at", sa.DateTime(), nullable=True),
+        sa.Column("demultiplexing_completed_at", sa.DateTime(), nullable=True),
+    )
+
+
+def downgrade():
+
+    op.drop_table("illumina_run_metrics")

alembic/versions/2024_05_17_fe23de4ed528_add_illumina_flow_cell.py

@@ -0,0 +1,31 @@
+"""add_illumina_flow_cell
+
+Revision ID: fe23de4ed528
+Revises: 6e6c36d5157b
+Create Date: 2024-05-17 15:09:12.088324
+
+"""
+
+import sqlalchemy as sa
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "fe23de4ed528"
+down_revision = "6e6c36d5157b"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.create_table(
+        "illumina_flow_cell",
+        sa.Column(
+            "id", sa.Integer(), sa.ForeignKey("run_device.id"), nullable=False, primary_key=True
+        ),
+        sa.Column("model", sa.String(length=32), nullable=False),
+    )
+
+
+def downgrade():
+    op.drop_table("illumina_flow_cell")

alembic/versions/2024_05_21_5fd7e8758fb1_add_autoincrement_to_device_tables.py

@@ -0,0 +1,143 @@
+"""add_autoincrement_to_device_tables
+
+Revision ID: 5fd7e8758fb1
+Revises: fe23de4ed528
+Create Date: 2024-05-21 09:25:47.751986
+
+"""
+
+import sqlalchemy as sa
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "5fd7e8758fb1"
+down_revision = "fe23de4ed528"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # Modify illumina flow cell primary key
+    op.drop_constraint(
+        constraint_name="illumina_flow_cell_ibfk_1",
+        table_name="illumina_flow_cell",
+        type_="foreignkey",
+    )
+    op.drop_constraint(constraint_name="fk_device_id", table_name="run_metrics", type_="foreignkey")
+    op.execute("ALTER TABLE run_device MODIFY COLUMN id INT NOT NULL AUTO_INCREMENT")
+    op.alter_column(
+        "illumina_flow_cell", "model", existing_type=sa.String(length=32), nullable=True
+    )
+    op.create_foreign_key(
+        constraint_name="fk_device_id",
+        source_table="run_metrics",
+        referent_table="run_device",
+        local_cols=["device_id"],
+        remote_cols=["id"],
+    )
+    op.create_foreign_key(
+        constraint_name="illumina_flow_cell_ibfk_1",
+        source_table="illumina_flow_cell",
+        referent_table="run_device",
+        local_cols=["id"],
+        remote_cols=["id"],
+    )
+
+    # Modify run metrics primary key
+    op.drop_constraint(
+        constraint_name="illumina_sequencing_metrics_ibfk_1",
+        table_name="illumina_sequencing_metrics",
+        type_="foreignkey",
+    )
+    op.execute("ALTER TABLE run_metrics MODIFY COLUMN id INT NOT NULL AUTO_INCREMENT")
+    op.create_foreign_key(
+        constraint_name="illumina_sequencing_metrics_ibfk_1",
+        source_table="illumina_sequencing_metrics",
+        referent_table="run_metrics",
+        local_cols=["id"],
+        remote_cols=["id"],
+    )
+    op.create_foreign_key(
+        constraint_name="fk_run_metrics_id",
+        source_table="sample_run_metrics",
+        referent_table="run_metrics",
+        local_cols=["run_metrics_id"],
+        remote_cols=["id"],
+    )
+
+    # Modify sample run metrics primary key
+    op.drop_constraint(
+        constraint_name="illumina_sample_run_metrics_ibfk_1",
+        table_name="illumina_sample_run_metrics",
+        type_="foreignkey",
+    )
+    op.execute("ALTER TABLE sample_run_metrics MODIFY COLUMN id INT NOT NULL AUTO_INCREMENT")
+    op.create_foreign_key(
+        constraint_name="illumina_sample_run_metrics_ibfk_1",
+        source_table="illumina_sample_run_metrics",
+        referent_table="sample_run_metrics",
+        local_cols=["id"],
+        remote_cols=["id"],
+    )
+
+
+def downgrade():
+    # Downgrade illumina flow cell primary key
+    op.drop_constraint(
+        constraint_name="illumina_flow_cell_ibfk_1",
+        table_name="illumina_flow_cell",
+        type_="foreignkey",
+    )
+    op.drop_constraint(constraint_name="fk_device_id", table_name="run_metrics", type_="foreignkey")
+    op.alter_column(
+        "illumina_flow_cell", "model", existing_type=sa.String(length=32), nullable=False
+    )
+    op.execute("ALTER TABLE run_device MODIFY COLUMN id INT NOT NULL")
+    op.create_foreign_key(
+        constraint_name="fk_device_id",
+        source_table="run_metrics",
+        referent_table="run_device",
+        local_cols=["device_id"],
+        remote_cols=["id"],
+    )
+    op.create_foreign_key(
+        constraint_name="illumina_flow_cell_ibfk_1",
+        source_table="illumina_flow_cell",
+        referent_table="run_device",
+        local_cols=["id"],
+        remote_cols=["id"],
+    )
+
+    # Downgrade illumina run metrics primary key
+    op.drop_constraint(
+        constraint_name="fk_run_metrics_id", table_name="sample_run_metrics", type_="foreignkey"
+    )
+    op.drop_constraint(
+        constraint_name="illumina_sequencing_metrics_ibfk_1",
+        table_name="illumina_sequencing_metrics",
+        type_="foreignkey",
+    )
+    op.execute("ALTER TABLE run_metrics MODIFY COLUMN id INT NOT NULL")
+    op.create_foreign_key(
+        constraint_name="illumina_sequencing_metrics_ibfk_1",
+        source_table="illumina_sequencing_metrics",
+        referent_table="run_metrics",
+        local_cols=["id"],
+        remote_cols=["id"],
+    )
+
+    # Downgrade illumina run sample metrics primary key
+    op.drop_constraint(
+        constraint_name="illumina_sample_run_metrics_ibfk_1",
+        table_name="illumina_sample_run_metrics",
+        type_="foreignkey",
+    )
+    op.execute("ALTER TABLE sample_run_metrics MODIFY COLUMN id INT NOT NULL")
+    op.create_foreign_key(
+        constraint_name="illumina_sample_run_metrics_ibfk_1",
+        source_table="illumina_sample_run_metrics",
+        referent_table="sample_run_metrics",
+        local_cols=["id"],
+        remote_cols=["id"],
+    )

alembic/versions/2024_05_22_18e3b2aba252_add_yield_columns.py

@@ -0,0 +1,84 @@
+"""2024_05_22_add_yield_columns
+
+Revision ID: 18e3b2aba252
+Revises: 5fd7e8758fb1
+Create Date: 2024-05-22 14:01:15.197675
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "18e3b2aba252"
+down_revision = "5fd7e8758fb1"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+
+    # rename table IlluminaSampleRunMetrics to IlluminaSampleSequencingMetrics
+    op.rename_table(
+        old_table_name="illumina_sample_run_metrics",
+        new_table_name="illumina_sample_sequencing_metrics",
+    )
+    # add column yield
+    op.add_column(
+        table_name="illumina_sample_sequencing_metrics",
+        column=sa.Column("yield", sa.Integer(), nullable=True),
+    )
+    # add column yield_q30
+    op.add_column(
+        table_name="illumina_sample_sequencing_metrics",
+        column=sa.Column("yield_q30", sa.Float(), nullable=True),
+    )
+    # rename  table run metrics to InstrumentRun
+    op.rename_table(
+        old_table_name="run_metrics",
+        new_table_name="instrument_run",
+    )
+    # on SampleRunMetrics change run_metrics_id to instrument_run_id
+    op.alter_column(
+        table_name="sample_run_metrics",
+        column_name="run_metrics_id",
+        new_column_name="instrument_run_id",
+        type_=sa.Integer(),
+    )
+    # rename illumina_sequencing_metrics to illumina_sequencing_run
+    op.rename_table(
+        old_table_name="illumina_sequencing_metrics",
+        new_table_name="illumina_sequencing_run",
+    )
+
+
+def downgrade():
+    # rename illumina_sequencing_metrics to illumina_sequencing_run
+    op.rename_table(
+        new_table_name="illumina_sequencing_metrics",
+        old_table_name="illumina_sequencing_run",
+    )
+
+    # on SampleRunMetrics change run_metrics_id to instrument_run_id
+    op.alter_column(
+        table_name="sample_run_metrics",
+        new_column_name="run_metrics_id",
+        column_name="instrument_run_id",
+        type_=sa.Integer(),
+    )
+    # rename run metrics -> InstrumentRun
+    op.rename_table(
+        new_table_name="run_metrics",
+        old_table_name="instrument_run",
+    )
+
+    # drop columns yield and yield_q30
+    op.drop_column(table_name="illumina_sample_sequencing_metrics", column_name="yield")
+    op.drop_column(table_name="illumina_sample_sequencing_metrics", column_name="yield_q30")
+
+    # rename table IlluminaSampleSequencingMetrics to IlluminaSampleRunMetrics
+    op.rename_table(
+        new_table_name="illumina_sample_run_metrics",
+        old_table_name="illumina_sample_sequencing_metrics",
+    )

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "60.7.18"
+__version__ = "60.8.7"

cg/apps/loqus.py

@@ -109,4 +109,4 @@ def get_nr_of_variants_in_file(self) -> dict[str, int]:
         return {"variants": nr_of_variants}
 
     def __repr__(self):
-        return f"LoqusdbAPI(binary_path={Path(self.binary_path).stem}, config_path={Path(self.config_path).stem})"
+        return f"LoqusdbAPI(binary_path={Path(self.binary_path).name}, config_path={Path(self.config_path).name})"