Snakemake logger improvement and small fixed to the Workflow constructor

tests/unit/common/test_workflow.py

@@ -33,7 +33,8 @@ def workflow(self) -> Workflow:
         return Workflow(
             name="Workflow Test",
             makespan=100.0,
-            executed_at=str(datetime.now().astimezone().isoformat())
+            executed_at=str(datetime.now().astimezone().isoformat()),
+            runtime_system_name="WfCommons",
         )
 
     @pytest.mark.unit
@@ -62,7 +63,7 @@ def test_workflow_creation(self, workflow: Workflow) -> None:
             },
             "runtimeSystem": {
                 "name": "WfCommons",
-                "version": f"{__version__}",
+                "version": f"unknown",
                 "url": f"https://docs.wfcommons.org/en/v{__version__}/"
             }
         }

wfcommons/common/workflow.py

@@ -71,7 +71,7 @@ def __init__(self,
         self.created_at: str = str(datetime.now().astimezone().isoformat())
         self.schema_version: str = f"{__schema_version__}"
         self.runtime_system_name: Optional[str] = "WfCommons" if not runtime_system_name else runtime_system_name
-        self.runtime_system_version: Optional[str] = str(__version__) if not runtime_system_version else runtime_system_version
+        self.runtime_system_version: Optional[str] = "unknown" if not runtime_system_version else runtime_system_version
         self.runtime_system_url: Optional[str] = f"https://docs.wfcommons.org/en/v{__version__}/" if not runtime_system_url else runtime_system_url
         self.executed_at: Optional[str] = str(datetime.now().astimezone().isoformat()) if not executed_at else executed_at
         self.makespan: Optional[float] = makespan

wfcommons/wfinstances/logs/snakemake.py

@@ -47,6 +47,8 @@ class SnakemakeLogsParser(LogsParser):
     :param path_prefix_rewrite: A tuple that specifies that a file path prefix(for the workflow data files)
        should be replaced by another prefix (this is useful when the workflow execution was on a
        different machine than the log parsing)
+    :param snakemake_version: The Snakemake version (e.g., "9.20.0")
+    :type snakemake_version: str
     """
 
     def __init__(self,
@@ -55,7 +57,8 @@ def __init__(self,
                  description: Optional[str] = None,
                  logger: Optional[Logger] = None,
                  rules_to_ignore: Optional[list[str]] = None,
-                 path_prefix_rewrite: Optional[tuple[str, str]] = None
+                 path_prefix_rewrite: Optional[tuple[str, str]] = None,
+                 snakemake_version: Optional[str] = "unknown"
                  ) -> None:
         """Create an object of the Snakemake parser."""
 
@@ -69,6 +72,7 @@ def __init__(self,
 
         self.execution_dir : pathlib.Path = execution_dir
         self.snkmt_db: pathlib.Path = snkmt_db
+        self.snakemake_version: str = snakemake_version
 
         self.file_map = {}
         self.file_objects = {}
@@ -99,6 +103,7 @@ def build_workflow(self, workflow_name: Optional[str] = None) -> Workflow:
         self.workflow = Workflow(name=self.workflow_name,
                                  description=self.description,
                                  runtime_system_name=self.wms_name,
+                                 runtime_system_version=self.snakemake_version,
                                  runtime_system_url=self.wms_url)
 
         # Parse the sqlite db for to identify rules
@@ -111,13 +116,14 @@ def build_workflow(self, workflow_name: Optional[str] = None) -> Workflow:
         self._create_tasks()
 
         # Set the workflow's makespan
-        workflow_start_time = math.inf
-        workflow_end_time = 0
-        for task in self.workflow.tasks.values():
-            task_start_time = datetime.fromisoformat(task.start_time).timestamp()
-            task_end_time = task_start_time + task.runtime
-            workflow_start_time = min(task_start_time, workflow_start_time)
-            workflow_end_time = max(task_end_time, workflow_end_time)
+        conn = sqlite3.connect(self.snkmt_db)
+        cursor = conn.cursor()
+        cursor.execute("SELECT * FROM workflows")
+        rows = cursor.fetchall()
+        if len(rows) != 1:
+            raise SystemError("The SQLite database has more than one entry in the workflows table")
+        workflow_start_time = datetime.fromisoformat(rows[0][2]).timestamp()
+        workflow_end_time = datetime.fromisoformat(rows[0][4]).timestamp()
         self.workflow.makespan = workflow_end_time - workflow_start_time
 
         return self.workflow