Update Neo4j to 5.x

beeflow/client/core.py

@@ -590,7 +590,7 @@ def pull_deps(outdir: str = typer.Option('.', '--outdir', '-o',
     """Pull required BEE containers and store in outdir."""
     load_check_charliecloud()
     neo4j_path = os.path.join(os.path.realpath(outdir), 'neo4j.tar.gz')
-    pull_to_tar('neo4j:3.5.22', neo4j_path)
+    pull_to_tar('neo4j:5.17', neo4j_path)
     redis_path = os.path.join(os.path.realpath(outdir), 'redis.tar.gz')
     pull_to_tar('redis', redis_path)
     print()

beeflow/common/gdb/neo4j_cypher.py

@@ -239,119 +239,119 @@ def get_task_by_id(tx, task_id):
 
     :param task_id: the task's ID
     :type task_id: str
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     task_query = "MATCH (t:Task {id: $task_id}) RETURN t"
 
-    return tx.run(task_query, task_id=task_id).single()
+    return tx.run(task_query, task_id=task_id).single()['t']
 
 
 def get_task_hints(tx, task_id):
     """Get task hints from the Neo4j database by the task's ID.
 
     :param task_id: the task's ID
     :type task_id: str
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     hints_query = "MATCH (:Task {id: $task_id})<-[:HINT_OF]-(h:Hint) RETURN h"
 
-    return tx.run(hints_query, task_id=task_id)
+    return [rec['h'] for rec in tx.run(hints_query, task_id=task_id)]
 
 
 def get_task_requirements(tx, task_id):
     """Get task requirements from the Neo4j database by the task's ID.
 
     :param task_id: the task's ID
     :type task_id: str
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     reqs_query = "MATCH (:Task {id: $task_id})<-[:REQUIREMENT_OF]-(r:Requirement) RETURN r"
 
-    return tx.run(reqs_query, task_id=task_id)
+    return [rec['r'] for rec in tx.run(reqs_query, task_id=task_id)]
 
 
 def get_task_inputs(tx, task_id):
     """Get task inputs from the Neo4j database by the task's ID.
 
     :param task_id: the task's ID
     :type task_id: str
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     inputs_query = "MATCH (:Task {id: $task_id})<-[:INPUT_OF]-(i:Input) RETURN i"
 
-    return tx.run(inputs_query, task_id=task_id)
+    return [rec['i'] for rec in tx.run(inputs_query, task_id=task_id)]
 
 
 def get_task_outputs(tx, task_id):
     """Get task outputs from the Neo4j database by the task's ID.
 
     :param task_id: the task's ID
     :type task_id: str
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     outputs_query = "MATCH (:Task {id: $task_id})<-[:OUTPUT_OF]-(o:Output) RETURN o"
 
-    return tx.run(outputs_query, task_id=task_id)
+    return [rec['o'] for rec in tx.run(outputs_query, task_id=task_id)]
 
 
 def get_workflow_description(tx):
     """Get the workflow description from the Neo4j database.
 
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     workflow_desc_query = "MATCH (w:Workflow) RETURN w"
 
-    return tx.run(workflow_desc_query).single()
+    return tx.run(workflow_desc_query).single()['w']
 
 
 def get_workflow_tasks(tx):
     """Get workflow tasks from the Neo4j database.
 
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     workflow_query = "MATCH (t:Task) RETURN t"
 
-    return tx.run(workflow_query)
+    return [rec['t'] for rec in tx.run(workflow_query)]
 
 
 def get_workflow_requirements(tx):
     """Get workflow requirements from the Neo4j database.
 
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     requirements_query = "MATCH (:Workflow)<-[:REQUIREMENT_OF]-(r:Requirement) RETURN r"
 
-    return tx.run(requirements_query)
+    return [rec['r'] for rec in tx.run(requirements_query)]
 
 
 def get_workflow_hints(tx):
     """Get workflow hints from the Neo4j database.
 
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     hints_query = "MATCH (:Workflow)<-[:HINT_OF]-(h:Hint) RETURN h"
 
-    return tx.run(hints_query)
+    return [rec['h'] for rec in tx.run(hints_query)]
 
 
 def get_workflow_inputs(tx):
     """Get workflow inputs from the Neo4j database.
 
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     inputs_query = "MATCH (:Workflow)<-[:INPUT_OF]-(i:Input) RETURN i"
 
-    return tx.run(inputs_query)
+    return [rec['i'] for rec in tx.run(inputs_query)]
 
 
 def get_workflow_outputs(tx):
     """Get workflow outputs from the Neo4j database.
 
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     outputs_query = "MATCH (:Workflow)<-[:OUTPUT_OF]-(o:Output) RETURN o"
 
-    return tx.run(outputs_query)
+    return [rec['o'] for rec in tx.run(outputs_query)]
 
 
 def get_workflow_state(tx):
@@ -378,23 +378,23 @@ def set_workflow_state(tx, state):
 def get_ready_tasks(tx):
     """Get all tasks that are ready to execute.
 
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     get_ready_query = "MATCH (:Metadata {state: 'READY'})-[:DESCRIBES]->(t:Task) RETURN t"
 
-    return tx.run(get_ready_query)
+    return [rec['t'] for rec in tx.run(get_ready_query)]
 
 
 def get_dependent_tasks(tx, task):
     """Get the tasks that depend on a specified task.
 
     :param task: the task whose dependencies to obtain
     :type task: Task
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     dependents_query = "MATCH (t:Task)-[:DEPENDS_ON]->(:Task {id: $task_id}) RETURN t"
 
-    return tx.run(dependents_query, task_id=task.id)
+    return [rec['t'] for rec in tx.run(dependents_query, task_id=task.id)]
 
 
 def get_task_state(tx, task):
@@ -428,11 +428,11 @@ def get_task_metadata(tx, task):
 
     :param task: the task whose metadata to get
     :type task: Task
-    :rtype: BoltStatementResult
+    :rtype: neo4j.Result
     """
     metadata_query = "MATCH (m:Metadata)-[:DESCRIBES]->(:Task {id: $task_id}) RETURN m"
 
-    return tx.run(metadata_query, task_id=task.id).single()
+    return dict(tx.run(metadata_query, task_id=task.id).single()['m'])
 
 
 def set_task_metadata(tx, task, metadata):
@@ -466,7 +466,7 @@ def get_task_input(tx, task, input_id):
     input_query = ("MATCH (t:Task {id: $task_id})<-[:INPUT_OF]-(i:Input {id: $input_id}) "
                    "RETURN i")
 
-    return tx.run(input_query, task_id=task.id, input_id=input_id).single()
+    return dict(tx.run(input_query, task_id=task.id, input_id=input_id).single()['i'])
 
 
 def set_task_input(tx, task, input_id, value):
@@ -496,7 +496,7 @@ def get_task_output(tx, task, output_id):
     output_query = ("MATCH (:Task {id: $task_id})<-[:OUTPUT_OF]-(o:Output {id: $output_id}) "
                     "RETURN o")
 
-    return tx.run(output_query, task_id=task.id, output_id=output_id).single()
+    return dict(tx.run(output_query, task_id=task.id, output_id=output_id).single()['o'])
 
 
 def set_task_output(tx, task, output_id, value):

beeflow/common/gdb/neo4j_driver.py

@@ -6,7 +6,7 @@
 """
 
 from neo4j import GraphDatabase as Neo4jDatabase
-from neobolt.exceptions import ServiceUnavailable
+from neo4j.exceptions import ServiceUnavailable
 
 from beeflow.common.gdb.gdb_driver import GraphDatabaseDriver
 from beeflow.common.gdb import neo4j_cypher as tx
@@ -307,7 +307,7 @@ def get_task_input(self, task, input_id):
         :rtype: StepInput
         """
         input_record = self._read_transaction(tx.get_task_input, task=task, input_id=input_id)
-        return _reconstruct_task_input(input_record["i"])
+        return _reconstruct_task_input(input_record)
 
     def set_task_input(self, task, input_id, value):
         """Set the value of a task input.
@@ -330,7 +330,7 @@ def get_task_output(self, task, output_id):
         :rtype: StepOutput
         """
         output_record = self._read_transaction(tx.get_task_output, task=task, output_id=output_id)
-        return _reconstruct_task_output(output_record["o"])
+        return _reconstruct_task_output(output_record)
 
     def set_task_output(self, task, output_id, value):
         """Set the value of a task output.
@@ -401,13 +401,13 @@ def _get_task_data_tuples(self, task_records):
         with self._driver.session() as session:
             trecords = list(task_records)
             hint_records = [session.read_transaction(tx.get_task_hints,
-                            task_id=rec["t"]["id"]) for rec in trecords]
+                            task_id=rec["id"]) for rec in trecords]
             req_records = [session.read_transaction(tx.get_task_requirements,
-                           task_id=rec["t"]["id"]) for rec in trecords]
+                           task_id=rec["id"]) for rec in trecords]
             input_records = [session.read_transaction(tx.get_task_inputs,
-                             task_id=rec["t"]["id"]) for rec in trecords]
+                             task_id=rec["id"]) for rec in trecords]
             output_records = [session.read_transaction(tx.get_task_outputs,
-                              task_id=rec["t"]["id"]) for rec in trecords]
+                              task_id=rec["id"]) for rec in trecords]
 
         hints = [_reconstruct_hints(hint_record) for hint_record in hint_records]
         reqs = [_reconstruct_requirements(req_record) for req_record in req_records]
@@ -447,9 +447,8 @@ def _reconstruct_requirements(req_records):
     :type req_records: BoltStatementResult
     :rtype: list of Requirement
     """
-    recs = [req_record["r"] for req_record in req_records]
     return [Requirement(rec["class"], {k: v for k, v in rec.items() if k != "class"})
-            for rec in recs]
+            for rec in req_records]
 
 
 def _reconstruct_hints(hint_records):
@@ -459,8 +458,8 @@ def _reconstruct_hints(hint_records):
     :type hint_records: BoltStatementResult
     :rtype: list of Hint
     """
-    recs = [hint_record["h"] for hint_record in hint_records]
-    return [Hint(rec["class"], {k: v for k, v in rec.items() if k != "class"}) for rec in recs]
+    return [Hint(rec["class"], {k: v for k, v in rec.items() if k != "class"})
+            for rec in hint_records]
 
 
 def _reconstruct_workflow_inputs(input_records):
@@ -470,8 +469,7 @@ def _reconstruct_workflow_inputs(input_records):
     :type input_records: BoltStatementResult
     :rtype: list of InputParameter
     """
-    recs = [input_record["i"] for input_record in input_records]
-    return [InputParameter(rec["id"], rec["type"], rec["value"]) for rec in recs]
+    return [InputParameter(rec["id"], rec["type"], rec["value"]) for rec in input_records]
 
 
 def _reconstruct_workflow_outputs(output_records):
@@ -481,8 +479,8 @@ def _reconstruct_workflow_outputs(output_records):
     :type output_records: BoltStatementResult
     :rtype: list of OutputParameter
     """
-    recs = [output_record["o"] for output_record in output_records]
-    return [OutputParameter(rec["id"], rec["type"], rec["value"], rec["source"]) for rec in recs]
+    return [OutputParameter(rec["id"], rec["type"], rec["value"], rec["source"])
+            for rec in output_records]
 
 
 def _reconstruct_task_inputs(input_records):
@@ -492,8 +490,7 @@ def _reconstruct_task_inputs(input_records):
     :type input_records: BoltStatementResult
     :rtype: list of StepInput
     """
-    recs = [input_record["i"] for input_record in input_records]
-    return [_reconstruct_task_input(rec) for rec in recs]
+    return [_reconstruct_task_input(rec) for rec in input_records]
 
 
 def _reconstruct_task_input(rec):
@@ -514,8 +511,7 @@ def _reconstruct_task_outputs(output_records):
     :type output_records: BoltStatementResult
     :rtype: list of StepOutput
     """
-    recs = [output_record["o"] for output_record in output_records]
-    return [_reconstruct_task_output(rec) for rec in recs]
+    return [_reconstruct_task_output(rec) for rec in output_records]
 
 
 def _reconstruct_task_output(rec):
@@ -543,9 +539,8 @@ def _reconstruct_workflow(workflow_record, hints, requirements, inputs, outputs)
     :type outputs: list of OutputParameter
     :rtype: Workflow
     """
-    rec = workflow_record["w"]
-    return Workflow(name=rec["name"], hints=hints, requirements=requirements, inputs=inputs,
-                    outputs=outputs, workflow_id=rec["id"])
+    return Workflow(name=workflow_record["name"], hints=hints, requirements=requirements,
+                    inputs=inputs, outputs=outputs, workflow_id=workflow_record["id"])
 
 
 def _reconstruct_task(task_record, hints, requirements, inputs, outputs):
@@ -563,10 +558,10 @@ def _reconstruct_task(task_record, hints, requirements, inputs, outputs):
     :type outputs: list of StepOutput
     :rtype: Task
     """
-    rec = task_record["t"]
-    return Task(name=rec["name"], base_command=rec["base_command"], hints=hints,
-                requirements=requirements, inputs=inputs, outputs=outputs, stdout=rec["stdout"],
-                stderr=rec["stderr"], workflow_id=rec["workflow_id"], task_id=rec["id"])
+    return Task(name=task_record["name"], base_command=task_record["base_command"],
+                hints=hints, requirements=requirements, inputs=inputs, outputs=outputs,
+                stdout=task_record["stdout"], stderr=task_record["stderr"],
+                workflow_id=task_record["workflow_id"], task_id=task_record["id"])
 
 
 def _reconstruct_metadata(metadata_record):
@@ -578,8 +573,7 @@ def _reconstruct_metadata(metadata_record):
     :type keys: iterable of str
     :rtype: dict
     """
-    rec = metadata_record["m"]
-    return {key: val for key, val in rec.items() if key != "state"}
+    return {key: val for key, val in metadata_record.items() if key != "state"}
 
 # Ignore E1129: External module is missing proper resource context manager methods.
 # pylama:ignore=E1129

beeflow/wf_manager/common/dep_manager.py

@@ -95,11 +95,11 @@ def setup_gdb_configs(mount_dir, bolt_port, http_port, https_port):
     with open(gdb_configfile, "rt", encoding="utf8") as cfile:
         data = cfile.read()
 
-    bolt_config = r'#(dbms.connector.bolt.listen_address=):[0-9]*'
+    bolt_config = r'#(server.bolt.listen_address=):[0-9]*'
     data = re.sub(bolt_config, rf'\1:{bolt_port}', data)
-    http_config = r'#(dbms.connector.http.listen_address=):[0-9]*'
+    http_config = r'#(server.http.listen_address=):[0-9]*'
     data = re.sub(http_config, rf'\1:{http_port}', data)
-    https_config = r'#(dbms.connector.https.listen_address=):[0-9]*'
+    https_config = r'#(server.https.listen_address=):[0-9]*'
     data = re.sub(https_config, rf'\1:{https_port}', data)
     with open(gdb_configfile, "wt", encoding="utf8") as cfile:
         cfile.write(data)
@@ -155,7 +155,7 @@ def start_gdb(mount_dir, bolt_port, http_port, https_port, reexecute=False):
     container_path = get_container_dir()
     if not reexecute:
         try:
-            command = ['neo4j-admin', 'set-initial-password', str(db_password)]
+            command = ['neo4j-admin', 'dbms', 'set-initial-password', str(db_password)]
             subprocess.run([
                 "ch-run",
                 "--set-env=" + container_path + "/ch/environment",
@@ -187,7 +187,8 @@ def start_gdb(mount_dir, bolt_port, http_port, https_port, reexecute=False):
                                "--", *command
                                ], stdout=subprocess.PIPE, stderr=subprocess.PIPE) as proc:
             output = proc.stdout.read().decode('utf-8')
-            pid = re.search(r'pid ([0-9]*)', output).group(1)
+            dep_log.info(output)
+            pid = re.search(r'\(pid:([0-9]*)\)', output).group(1)
             return pid
     except FileNotFoundError:
         dep_log.error("Neo4j failed to start.")