Merge branch 'issue764/add-logging-to-wfi' into develop

Add logging to WFI: enable logging in gdb_driver neo4j_driver and neo4j_cypher

beeflow/common/gdb/gdb_driver.py

@@ -1,6 +1,9 @@
 """Abstract base class for the handling of workflow DAGs."""
 
 from abc import ABC, abstractmethod
+from beeflow.common import log as bee_logging
+
+log = bee_logging.setup(__name__)
 
 
 class GraphDatabaseDriver(ABC):

beeflow/common/gdb/neo4j_cypher.py

@@ -1,6 +1,9 @@
 """Neo4j/Cypher transaction functions used by the Neo4jDriver class."""
 
 from re import fullmatch
+from beeflow.common import log as bee_logging
+
+log = bee_logging.setup(__name__)
 
 
 def create_workflow_node(tx, workflow):

beeflow/common/gdb/neo4j_driver.py

@@ -12,6 +12,9 @@
 from beeflow.common.gdb import neo4j_cypher as tx
 from beeflow.common.wf_data import (Workflow, Task, Requirement, Hint,
                                     InputParameter, OutputParameter, StepInput, StepOutput)
+from beeflow.common import log as bee_logging
+
+log = bee_logging.setup(__name__)
 
 # Default Neo4j authentication
 # We may want to instead get these from a config at some point
@@ -51,6 +54,7 @@ def __init__(self, user=DEFAULT_USER, password=DEFAULT_PASSWORD, **kwargs):
             # Connect to the Neo4j database using the Neo4j proprietary driver
             self._driver = Neo4jDatabase.driver(uri, auth=(user, password))
         except ServiceUnavailable as sue:
+            log.error("Neo4j database is unavailable")
             raise Neo4JNotRunning("Neo4j database is unavailable") from sue
 
     def initialize_workflow(self, workflow):

beeflow/common/wf_interface.py

@@ -4,6 +4,9 @@
 """
 
 import re
+from beeflow.common import log as bee_logging
+
+log = bee_logging.setup(__name__)
 
 
 class WorkflowInterface:
@@ -33,6 +36,7 @@ def initialize_workflow(self, workflow):
         :type workflow: Workflow
         """
         if self.workflow_loaded():
+            log.error("attempt to re-initialize existing workflow")
             raise RuntimeError("attempt to re-initialize existing workflow")
         if workflow.requirements is None:
             workflow.requirements = []
@@ -107,6 +111,7 @@ def restart_task(self, task, checkpoint_file):
                 self.set_workflow_state("FAILED")
                 return None
         else:
+            log.error("invalid task for checkpoint restart")
             raise ValueError("invalid task for checkpoint restart")
 
         new_task = task.copy(new_id=True)