Fix(tests) Improve panel pytest (#2682)(patch)

### Added

- New test for the `panel` function

tests/cli/workflow/mip/conftest.py

@@ -14,7 +14,6 @@
 from cg.store.api.find_business_data import FindBusinessDataHandler
 from cg.store.api.status import StatusHandler
 from cg.store.models import Case
-from tests.store.conftest import case_obj
 from tests.store_helpers import StoreHelpers
 
 
@@ -192,3 +191,50 @@ def setup_mocks(
 
     mocker.patch.object(FindBusinessDataHandler, "are_all_flow_cells_on_disk")
     FindBusinessDataHandler.are_all_flow_cells_on_disk.return_value = True
+
+
+@pytest.fixture
+def scout_panel_output() -> str:
+    return """##genome_build=37
+##gene_panel=OMIM-AUTO,version=22.0,updated_at=2023-10-17,display_name=OMIM-AUTO
+##gene_panel=PANELAPP-GREEN,version=6.0,updated_at=2023-10-19,display_name=PanelApp Green Genes
+##contig=1
+##contig=2
+##contig=3
+##contig=4
+##contig=5
+##contig=6
+##contig=7
+##contig=8
+##contig=9
+##contig=10
+##contig=X
+##contig=Y
+##contig=MT
+#chromosome	gene_start	gene_stop	hgnc_id	hgnc_symbol
+1	568915	569121	44571	MTATP8P1
+1	860260	879955	28706	SAMD11
+2       162164549       162268228       16889   PSMD14
+2       162272605       162282381       11590   TBR1
+3       120315156       120321347       7699    NDUFB4
+3       120347020       120401418       4892    HGD
+4       185570767       185616117       26575   PRIMPOL
+4       185676749       185747972       3569    ACSL1
+5       473425  524447  11073   SLC9A3
+5       892758  919472  12307   TRIP13
+6       18224099        18265054        2768    DEK
+6       19837617        19840915        5363    ID4
+7       44256749        44374176        1461    CAMK2B
+7       44646171        44748665        8124    OGDH
+8       22993101        23021543        11907   TNFRSF10D
+8       23047965        23082639        11904   TNFRSF10A
+9       35099888        35103154        14559   STOML2
+9       35161999        35405335        12566   UNC13B
+10      23481256        23483181        23734   PTF1A
+10      25305587        25315593        26160   THNSL1
+X       154719776       154899605       18308   TMLHE
+X       155110956       155173433       11486   VAMP7
+Y       6778727 6959724 18502   TBL1Y
+Y       14813160        14972764        12633   USP9Y
+MT      577     647     7481    MT-TF
+MT      648     1601    7470    MT-RNR1"""

tests/cli/workflow/mip/test_cli_mip_base.py

@@ -2,6 +2,7 @@
 
 import logging
 
+import mock
 from _pytest.logging import LogCaptureFixture
 from click.testing import CliRunner
 from pytest_mock import MockFixture
@@ -83,7 +84,7 @@ def test_spring_decompression_needed_and_start_failed(
     assert result.exit_code == 0
 
     # THEN it should be announced that spring decompression is needed but fail to start
-    assert f"Decompression failed to start for" in caplog.text
+    assert "Decompression failed to start for" in caplog.text
 
 
 def test_spring_decompression_needed_and_cant_start(
@@ -120,7 +121,7 @@ def test_spring_decompression_needed_and_cant_start(
     assert result.exit_code == 0
 
     # THEN it should be announced that spring decompression is needed but fail to start
-    assert f"Decompression can not be started for" in caplog.text
+    assert "Decompression can not be started for" in caplog.text
 
 
 def test_decompression_cant_start_and_is_running(
@@ -157,7 +158,7 @@ def test_decompression_cant_start_and_is_running(
     assert result.exit_code == 0
 
     # THEN it should be announced that spring decompression is needed but fail to start
-    assert f"Decompression is running for" in caplog.text
+    assert "Decompression is running for" in caplog.text
 
 
 def test_case_needs_to_be_stored(
@@ -188,8 +189,14 @@ def test_case_needs_to_be_stored(
         mocker=mocker,
     )
 
-    # WHEN MIP analysis is started
-    result = cli_runner.invoke(start, [case.internal_id, "--dry-run"], obj=mip_dna_context)
+    # GIVEN that a panel is returned
+    with mock.patch.object(
+        mip_dna_context.scout_api,
+        "export_panels",
+        return_value=["OMIM-AUTO"],
+    ):
+        # WHEN MIP analysis is started
+        result = cli_runner.invoke(start, [case.internal_id, "--dry-run"], obj=mip_dna_context)
 
     # THEN command should run without errors
     assert result.exit_code == 0

tests/cli/workflow/mip/test_cli_mip_dna_panel.py

@@ -1,15 +1,36 @@
 """ Test the CLI for mip-dna panel"""
+from pathlib import Path
+
+import mock
+from click.testing import CliRunner
 
 from cg.cli.workflow.mip_dna.base import panel
+from cg.io.txt import read_txt
+from cg.meta.workflow.mip import MipAnalysisAPI
+from cg.models.cg_config import CGConfig
+from tests.conftest import create_process_response
+
+
+def test_panel_file_is_written(
+    case_id: str, cli_runner: CliRunner, mip_dna_context: CGConfig, scout_panel_output: str
+):
+    analysis_api: MipAnalysisAPI = mip_dna_context.meta_apis["analysis_api"]
 
+    # GIVEN a case
 
-def test_cg_workflow_mip_dna_panel(cli_runner, case_id, mip_dna_context):
-    """Test print the MIP dna panel command to console"""
+    # GIVEN that the scout command writes the panel to stdout
+    with mock.patch(
+        "cg.utils.commands.subprocess.run",
+        return_value=create_process_response(std_out=scout_panel_output),
+    ):
+        # WHEN creating a panel file
+        cli_runner.invoke(panel, [case_id], obj=mip_dna_context)
 
-    # GIVEN a cli function
+    panel_file = Path(analysis_api.root, case_id, "gene_panels.bed")
 
-    # WHEN we run a case in dry run mode
-    result = cli_runner.invoke(panel, [case_id], obj=mip_dna_context)
+    # THEN the file should exist
+    assert panel_file.exists()
 
-    # THEN the command should be printed
-    assert result.exit_code == 0
+    # THEN the file should contain the output from scout
+    file_content: str = read_txt(file_path=panel_file, read_to_string=True)
+    assert file_content == scout_panel_output

tests/conftest.py

@@ -7,6 +7,7 @@
 from copy import deepcopy
 from datetime import MAXYEAR, datetime, timedelta
 from pathlib import Path
+from subprocess import CompletedProcess
 from typing import Any, Generator, Union
 
 import pytest
@@ -2400,7 +2401,7 @@ def context_config(
             "tower_pipeline": "taxprofiler",
         },
         "scout": {
-            "binary_path": "echo",
+            "binary_path": "bin/scout",
             "config_path": "scout-stage.yaml",
         },
         "statina": {
@@ -3283,6 +3284,18 @@ def flow_cell_encryption_api(
     return flow_cell_encryption_api
 
 
+def create_process_response(
+    return_code: int = 0, args: str = "", std_out: str = "", std_err: str = ""
+) -> CompletedProcess:
+    """Returns a CompletedProcess object with default parameters."""
+    return CompletedProcess(
+        args=args,
+        returncode=return_code,
+        stderr=std_err.encode("utf-8"),
+        stdout=std_out.encode("utf-8"),
+    )
+
+
 # Downsample
 @pytest.fixture()
 def store_with_case_and_sample_with_reads(

tests/meta/backup/conftest.py

@@ -1,6 +1,5 @@
 import fnmatch
 from pathlib import Path
-from subprocess import CompletedProcess
 from typing import Callable
 
 import pytest
@@ -73,14 +72,3 @@ def archived_flow_cell() -> Path:
 def archived_key() -> Path:
     """Path of archived key"""
     return Path("/path/to/archived/encryption_key.key.gpg")
-
-
-def create_process_response(
-    return_code: int, args: str = "", std_out: str = "", std_err: str = ""
-) -> CompletedProcess:
-    return CompletedProcess(
-        args=args,
-        returncode=return_code,
-        stderr=std_err.encode("utf-8"),
-        stdout=std_out.encode("utf-8"),
-    )

tests/meta/backup/test_meta_pdc.py

@@ -17,7 +17,7 @@
 from cg.models.cg_config import CGConfig
 from cg.store import Store
 from cg.store.models import Flowcell
-from tests.meta.backup.conftest import create_process_response
+from tests.conftest import create_process_response
 from tests.store_helpers import StoreHelpers
 
 

tests/store/api/find/test_find_business_data.py

@@ -15,9 +15,9 @@
     Application,
     ApplicationLimitations,
     ApplicationVersion,
-    Customer,
     Case,
     CaseSample,
+    Customer,
     Flowcell,
     Invoice,
     Pool,
@@ -286,10 +286,10 @@ def test_are_all_flow_cells_on_disk_when_requested(
     case_id: str,
     helpers: StoreHelpers,
     sample: Sample,
+    request,
 ):
     """Test check if all flow cells for samples on a case is on disk when requested."""
     caplog.set_level(logging.DEBUG)
-
     # GIVEN a store with two flow cell
     helpers.add_flow_cell(
         store=base_store,