add raredisease to cli cg workflow (#2649)

### Added

- cli option: `cg workflow raredisease`

alembic/versions/9073c61bc72b_add_raredisease_to_analysis_options.py

@@ -0,0 +1,77 @@
+"""Add raredisease to analysis options
+
+Revision ID: 9073c61bc72b
+Revises: b6f00cc615cf
+Create Date: 2023-10-31 12:23:09.239741
+
+"""
+import sqlalchemy as sa
+from sqlalchemy.dialects import mysql
+from sqlalchemy.orm import declarative_base
+
+from alembic import op
+from cg.constants import Pipeline
+
+
+# revision identifiers, used by Alembic.
+revision = "9073c61bc72b"
+down_revision = "b6f00cc615cf"
+branch_labels = None
+depends_on = None
+
+Base = declarative_base()
+
+old_analysis_options = (
+    "balsamic",
+    "balsamic-pon",
+    "balsamic-qc",
+    "balsamic-umi",
+    "demultiplex",
+    "fastq",
+    "fluffy",
+    "microsalt",
+    "mip-dna",
+    "mip-rna",
+    "rnafusion",
+    "rsync",
+    "sars-cov-2",
+    "spring",
+    "taxprofiler",
+)
+new_analysis_options = sorted(old_analysis_options + ("raredisease",))
+
+old_analysis_enum = mysql.ENUM(*old_analysis_options)
+new_analysis_enum = mysql.ENUM(*new_analysis_options)
+
+
+class Analysis(Base):
+    __tablename__ = "analysis"
+    id = sa.Column(sa.types.Integer, primary_key=True)
+    pipeline = sa.Column(sa.types.Enum(*list(Pipeline)))
+
+
+class Family(Base):
+    __tablename__ = "family"
+    id = sa.Column(sa.types.Integer, primary_key=True)
+    data_analysis = sa.Column(sa.types.Enum(*list(Pipeline)))
+
+
+def upgrade():
+    op.alter_column("family", "data_analysis", type_=new_analysis_enum)
+    op.alter_column("analysis", "pipeline", type_=new_analysis_enum)
+
+
+def downgrade():
+    bind = op.get_bind()
+    session = sa.orm.Session(bind=bind)
+    for analysis in session.query(Analysis).filter(Analysis.pipeline == "raredisease"):
+        print(
+            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")
+        family.data_analysis = "mip-dna"
+    op.alter_column("family", "data_analysis", type_=old_analysis_enum)
+    op.alter_column("analysis", "pipeline", type_=old_analysis_enum)
+    session.commit()

cg/cli/workflow/base.py

@@ -13,6 +13,7 @@
 from cg.cli.workflow.mip_dna.base import mip_dna
 from cg.cli.workflow.mip_rna.base import mip_rna
 from cg.cli.workflow.mutant.base import mutant
+from cg.cli.workflow.raredisease.base import raredisease
 from cg.cli.workflow.rnafusion.base import rnafusion
 from cg.cli.workflow.taxprofiler.base import taxprofiler
 
@@ -32,5 +33,6 @@ def workflow():
 workflow.add_command(fluffy)
 workflow.add_command(mutant)
 workflow.add_command(rnafusion)
+workflow.add_command(raredisease)
 workflow.add_command(taxprofiler)
 workflow.add_command(fastq)

cg/cli/workflow/raredisease/__init__.py

@@ -0,0 +1 @@
+"""Init for module"""

cg/cli/workflow/raredisease/base.py

@@ -0,0 +1,21 @@
+"""CLI support to create config and/or start RAREDISEASE."""
+
+import logging
+
+import click
+
+from cg.constants.constants import MetaApis
+from cg.meta.workflow.analysis import AnalysisAPI
+from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
+
+LOG = logging.getLogger(__name__)
+
+
+@click.group(invoke_without_command=True)
+@click.pass_context
+def raredisease(context: click.Context) -> None:
+    """nf-core/raredisease analysis workflow."""
+    AnalysisAPI.get_help(context)
+    context.obj.meta_apis[MetaApis.ANALYSIS_API] = RarediseaseAnalysisAPI(
+        config=context.obj,
+    )

cg/meta/workflow/raredisease.py

@@ -0,0 +1,20 @@
+"""Module for Raredisease Analysis API."""
+
+import logging
+from cg.constants import Pipeline
+from cg.meta.workflow.nf_analysis import NfAnalysisAPI
+from cg.models.cg_config import CGConfig
+
+LOG = logging.getLogger(__name__)
+
+
+class RarediseaseAnalysisAPI(NfAnalysisAPI):
+    """Handles communication between RAREDISEASE processes
+    and the rest of CG infrastructure."""
+
+    def __init__(
+        self,
+        config: CGConfig,
+        pipeline: Pipeline = Pipeline.RAREDISEASE,
+    ):
+        super().__init__(config=config, pipeline=pipeline)

tests/cli/workflow/raredisease/conftest.py

@@ -0,0 +1,14 @@
+"""Fixtures for cli workflow raredisease tests"""
+
+import pytest
+from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
+from cg.models.cg_config import CGConfig
+
+
+@pytest.fixture(scope="function", name="raredisease_context")
+def fixture_raredisease_context(
+    cg_context: CGConfig,
+) -> CGConfig:
+    """Context to use in cli."""
+    cg_context.meta_apis["analysis_api"] = RarediseaseAnalysisAPI(config=cg_context)
+    return cg_context

tests/cli/workflow/raredisease/test_cli_raredisease_compound_commands.py

@@ -0,0 +1,25 @@
+import logging
+
+from _pytest.logging import LogCaptureFixture
+from click.testing import CliRunner
+from cg.cli.workflow.raredisease.base import (
+    raredisease,
+)
+from cg.constants import EXIT_SUCCESS
+from cg.models.cg_config import CGConfig
+
+
+def test_raredisease_no_args(cli_runner: CliRunner, raredisease_context: CGConfig):
+    """Test to see that running RAREDISEASE without options prints help and doesn't result in an error."""
+    # GIVEN no arguments or options besides the command call
+
+    # WHEN running command
+    result = cli_runner.invoke(raredisease, [], obj=raredisease_context)
+
+    # THEN command runs successfully
+    print(result.output)
+
+    assert result.exit_code == EXIT_SUCCESS
+
+    # THEN help should be printed
+    assert "help" in result.output