feat: release v16.0.1 (#1532)

### Removed - case_report.html from delivery command
Clinical-Genomics · Feb 10, 2025 · cff0826 · cff0826
1 parent 2580640
commit cff0826
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Showing 6 changed files with 10 additions and 69 deletions.
diff --git a/BALSAMIC/commands/report/deliver.py b/BALSAMIC/commands/report/deliver.py
@@ -1,22 +1,17 @@
 """Report deliver CLI command."""
 import logging
-import subprocess
-import sys
 from pathlib import Path
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List
 
 import click
 import snakemake
 from BALSAMIC.constants.constants import FileType
 
 from BALSAMIC.commands.options import (
-    OPTION_DISABLE_VARIANT_CALLER,
     OPTION_RULES_TO_DELIVER,
     OPTION_SAMPLE_CONFIG,
 )
-from BALSAMIC.constants.analysis import RunMode
 from BALSAMIC.models.config import ConfigModel
-from BALSAMIC.models.snakemake import SnakemakeExecutable
 from BALSAMIC.utils.cli import (
     get_snakefile,
     convert_deliverables_tags,
@@ -31,13 +26,11 @@
 @click.command(
     "deliver", short_help="Create a <case_id>.hk file with output analysis files"
 )
-@OPTION_DISABLE_VARIANT_CALLER
 @OPTION_RULES_TO_DELIVER
 @OPTION_SAMPLE_CONFIG
 @click.pass_context
 def deliver(
     context: click.Context,
-    disable_variant_caller: Optional[str],
     rules_to_deliver: List[str],
     sample_config: str,
 ):
@@ -48,33 +41,12 @@ def deliver(
     config_model: ConfigModel = ConfigModel(**config)
     output_dir: Path = Path(config_model.analysis.result, "delivery_report")
     output_dir.mkdir(exist_ok=True)
-    working_dir: Path = Path(
-        config_model.analysis.analysis_dir,
-        config_model.analysis.case_id,
-        "BALSAMIC_run",
-    )
-    html_report: Path = Path(output_dir, f"{config_model.analysis.case_id}_report.html")
+
     snakefile: Path = get_snakefile(
         analysis_type=config_model.analysis.analysis_type,
         analysis_workflow=config_model.analysis.analysis_workflow,
     )
 
-    LOG.info(f"Creating HTML report file: {html_report.as_posix()}")
-    snakemake_executable: SnakemakeExecutable = SnakemakeExecutable(
-        case_id=config_model.analysis.case_id,
-        config_path=sample_config,
-        disable_variant_caller=disable_variant_caller,
-        report_path=html_report,
-        run_analysis=True,
-        run_mode=RunMode.LOCAL,
-        snakefile=snakefile,
-        snakemake_options=["--quiet"],
-        working_dir=working_dir,
-    )
-    subprocess.check_output(
-        f"{sys.executable} -m {snakemake_executable.get_command()}".split(), shell=False
-    )
-
     LOG.info(f"Delivering analysis workflow: {config_model.analysis.analysis_workflow}")
     hk_file: Path = Path(output_dir, f"{config_model.analysis.case_id}.hk")
     delivery_ready_file: Path = Path(
@@ -92,17 +64,6 @@ def deliver(
         delivery_json=hk_deliverables, sample_config_dict=config
     )
 
-    # HTML analysis report
-    hk_deliverables.append(
-        {
-            "path": html_report.as_posix(),
-            "step": "balsamic_delivery",
-            "format": get_file_extension(html_report.as_posix()),
-            "tag": ["balsamic-report"],
-            "id": config_model.analysis.case_id,
-        }
-    )
-
     # Sample configuration file
     hk_deliverables.append(
         {

diff --git a/BALSAMIC/models/snakemake.py b/BALSAMIC/models/snakemake.py
@@ -41,7 +41,6 @@ class SnakemakeExecutable(BaseModel):
         profile (Optional[ClusterProfile])                           : Cluster profile to submit jobs.
         qos (Optional[QOS])                                          : QOS for sbatch jobs.
         quiet (Optional[bool])                                       : Quiet mode for snakemake.
-        report_path (Optional[Path])                                 : Snakemake generated report path.
         run_analysis (bool)                                          : Flag to run the actual analysis.
         run_mode (RunMode)                                           : Cluster run mode to execute analysis.
         script_dir (Optional[DirectoryPath])                         : Cluster profile scripts directory.
@@ -66,7 +65,6 @@ class SnakemakeExecutable(BaseModel):
     profile: Optional[ClusterProfile] = None
     qos: Optional[QOS] = None
     quiet: bool = False
-    report_path: Optional[Path] = None
     run_analysis: bool = False
     run_mode: RunMode
     script_dir: Optional[DirectoryPath] = None
@@ -113,12 +111,6 @@ def get_quiet_flag(self) -> str:
             return "--quiet"
         return ""
 
-    def get_report_path_option(self) -> str:
-        """Return string representation of the report_path option."""
-        if self.report_path:
-            return f"--report {self.report_path.as_posix()}"
-        return ""
-
     def get_run_analysis_flag(self) -> str:
         """Return string representation of the run_analysis flag."""
         if not self.run_analysis:
@@ -154,7 +146,6 @@ def get_command(self) -> str:
             f"{self.get_force_flag()} "
             f"{self.get_run_analysis_flag()} "
             f"{self.get_snakemake_cluster_options()} "
-            f"{self.get_report_path_option()} "
             f"{self.get_config_options()} "
             f"{self.get_snakemake_options_command()}"
         )

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,3 +1,11 @@
+[16.0.1]
+-------
+
+Removed:
+^^^^^^^^
+* remove snakemake case_report.html report creation https://github.com/Clinical-Genomics/BALSAMIC/pull/1530
+
+
 [16.0.0]
 -------
 

diff --git a/tests/commands/report/test_deliver.py b/tests/commands/report/test_deliver.py
@@ -35,8 +35,6 @@ def test_deliver_tumor_only_panel(
                 "deliver",
                 "--sample-config",
                 tumor_only_config,
-                "--disable-variant-caller",
-                "cnvkit",
             ]
         )
 

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -2469,7 +2469,6 @@ def fixture_snakemake_executable_validated_data(
         "profile": ClusterProfile.SLURM,
         "qos": QOS.HIGH,
         "quiet": True,
-        "report_path": None,
         "run_analysis": True,
         "run_mode": RunMode.CLUSTER,
         "script_dir": session_tmp_path,

diff --git a/tests/models/test_snakemake_models.py b/tests/models/test_snakemake_models.py
@@ -122,22 +122,6 @@ def test_quiet_flag(snakemake_executable: SnakemakeExecutable):
     assert quiet_flag == "--quiet"
 
 
-def test_get_report_path_option(
-    session_tmp_path: Path, snakemake_executable: SnakemakeExecutable
-):
-    """Test formatting of the report path option."""
-
-    # GIVEN a snakemake executable model with a report path option
-    snakemake_model: SnakemakeExecutable = copy.deepcopy(snakemake_executable)
-    snakemake_model.report_path = session_tmp_path
-
-    # WHEN calling the method
-    report_path_option: str = snakemake_model.get_report_path_option()
-
-    # THEN the expected format should be returned
-    assert report_path_option == f"--report {session_tmp_path.as_posix()}"
-
-
 def test_get_run_analysis_flag(snakemake_executable: SnakemakeExecutable):
     """Test formatting of the run analysis flag."""