diff --git a/beeflow/client/bee_client.py b/beeflow/client/bee_client.py index 7bc1b53e3..1dc03a9bb 100644 --- a/beeflow/client/bee_client.py +++ b/beeflow/client/bee_client.py @@ -41,6 +41,7 @@ logging.basicConfig(level=logging.WARNING) +logging.getLogger("neo4j").setLevel(logging.WARNING) WORKFLOW_MANAGER = 'bee_wfm/v1/jobs/' @@ -623,6 +624,14 @@ def reexecute(wf_name: str = typer.Argument(..., help='The workflow name'), return wf_id +@app.command() +def dag(wf_id: str = typer.Argument(..., callback=match_short_id)): + """Export a DAG of the workflow to a GraphML file.""" + wf_utils.export_dag(wf_id) + typer.secho(f"DAG for workflow {_short_id(wf_id)} has been exported successfully.", + fg=typer.colors.GREEN) + + @app.callback(invoke_without_command=True) def version_callback(version: bool = False): """Beeflow.""" diff --git a/beeflow/common/deps/neo4j_manager.py b/beeflow/common/deps/neo4j_manager.py index df0c58cde..298710cd5 100644 --- a/beeflow/common/deps/neo4j_manager.py +++ b/beeflow/common/deps/neo4j_manager.py @@ -23,6 +23,8 @@ run_dir = mount_dir + '/run' certs_dir = mount_dir + '/certificates' confs_dir = mount_dir + "/conf" +dags_dir = os.path.join(bee_workdir, 'dags') +graphmls_dir = dags_dir + "/graphmls" container_path = container_manager.get_container_dir('neo4j') log = bee_logging.setup('neo4j') @@ -59,6 +61,8 @@ def setup_mounts(): os.makedirs(mount_dir, exist_ok=True) os.makedirs(certs_dir, exist_ok=True) os.makedirs(run_dir, exist_ok=True) + os.makedirs(dags_dir, exist_ok=True) + os.makedirs(graphmls_dir, exist_ok=True) def setup_configs(bolt_port, http_port, https_port): @@ -86,6 +90,24 @@ def setup_configs(bolt_port, http_port, https_port): with open(gdb_configfile, "wt", encoding="utf8") as cfile: cfile.write(data) + apoc_configfile = os.path.join(confs_dir, "apoc.conf") + if not os.path.exists(apoc_configfile): + with open(apoc_configfile, "wt", encoding="utf8") as afile: + afile.write("apoc.export.file.enabled=true\n") + log.info(f"Created {apoc_configfile} with apoc.export.file.enabled=true") + else: + with open(apoc_configfile, "rt", encoding="utf8") as afile: + apoc_data = afile.read() + + apoc_config = r'#?(apoc.export.file.enabled=)[^\n]*' + if re.search(apoc_config, apoc_data): + apoc_data = re.sub(apoc_config, r'apoc.export.file.enabled=true', apoc_data) + else: + apoc_data += "\napoc.export.file.enabled=true\n" + + with open(apoc_configfile, "wt", encoding="utf8") as afile: + afile.write(apoc_data) + def create_credentials(): """Create the password and set the logfiles in environment.""" @@ -95,10 +117,12 @@ def create_credentials(): subprocess.run([ "ch-run", "--set-env=" + container_path + "/ch/environment", + "--set-env=apoc.export.file.enabled=true", "-b", confs_dir + ":/var/lib/neo4j/conf", "-b", data_dir + ":/data", "-b", logs_dir + ":/logs", "-b", run_dir + ":/var/lib/neo4j/run", container_path, + "-W", "-b", graphmls_dir + ":/var/lib/neo4j/import", "--", *command ], check=True) except subprocess.CalledProcessError: @@ -112,11 +136,13 @@ def create_database(): proc = subprocess.Popen([ #noqa can't use with because returning "ch-run", "--set-env=" + container_path + "/ch/environment", + "--set-env=apoc.export.file.enabled=true", "-b", confs_dir + ":/var/lib/neo4j/conf", "-b", data_dir + ":/data", "-b", logs_dir + ":/logs", "-b", run_dir + ":/var/lib/neo4j/run", "-b", certs_dir + ":/var/lib/neo4j/certificates", + "-W", "-b", graphmls_dir + ":/var/lib/neo4j/import", container_path, "--", *command ], stdout=subprocess.PIPE, stderr=subprocess.PIPE) wait_gdb() diff --git a/beeflow/common/gdb/gdb_driver.py b/beeflow/common/gdb/gdb_driver.py index 9218dc06e..226b638d6 100644 --- a/beeflow/common/gdb/gdb_driver.py +++ b/beeflow/common/gdb/gdb_driver.py @@ -287,3 +287,7 @@ def workflow_completed(self): @abstractmethod def close(self): """Close the connection to the graph database.""" + + @abstractmethod + def export_graphml(self): + """Export a BEE workflow as a graphml.""" diff --git a/beeflow/common/gdb/generate_graph.py b/beeflow/common/gdb/generate_graph.py new file mode 100644 index 000000000..aa0cb73f8 --- /dev/null +++ b/beeflow/common/gdb/generate_graph.py @@ -0,0 +1,81 @@ +"""Module to make a png of a graph from a graphml file.""" + +import os +import networkx as nx +import graphviz + +from beeflow.common import paths + +bee_workdir = paths.workdir() +dags_dir = os.path.join(bee_workdir, 'dags') +graphmls_dir = dags_dir + "/graphmls" + + +def generate_viz(wf_id): + """Generate a PNG of a workflow graph from a GraphML file.""" + short_id = wf_id[:6] + graphml_path = graphmls_dir + "/" + short_id + ".graphml" + output_path = dags_dir + "/" + short_id + + # Load the GraphML file using NetworkX + graph = nx.read_graphml(graphml_path) + + # Initialize Graphviz graph + dot = graphviz.Digraph(comment='Hierarchical Graph') + + # Add nodes and edges using helper functions + add_nodes_to_dot(graph, dot) + add_edges_to_dot(graph, dot) + + # Render the graph and save as PNG + png_data = dot.pipe(format='png') + with open(output_path + ".png", "wb") as png_file: + png_file.write(png_data) + + +def add_nodes_to_dot(graph, dot): + """Add nodes from the graph to the Graphviz object with labels and colors.""" + label_to_color = { + ":Workflow": 'steelblue', + ":Output": 'mediumseagreen', + ":Metadata": 'skyblue', + ":Task": 'lightcoral', + ":Input": 'sandybrown', + ":Hint": 'plum', + ":Requirement": 'lightpink1' + } + + for node_id, attributes in graph.nodes(data=True): + label = attributes.get('labels', node_id) + node_label, color = get_node_label_and_color(label, attributes, label_to_color) + dot.node(node_id, label=node_label, style='filled', fillcolor=color) + + +def get_node_label_and_color(label, attributes, label_to_color): + """Return the appropriate node label and color based on node type.""" + label_to_attribute = { + ":Workflow": "Workflow", + ":Output": attributes.get('value', label), + ":Metadata": attributes.get('state', label), + ":Task": attributes.get('name', label), + ":Input": attributes.get('source', label), + ":Hint": attributes.get('class', label), + ":Requirement": attributes.get('class', label) + } + + # Check if the label is in the predefined labels + if label in label_to_attribute: + return label_to_attribute[label], label_to_color.get(label, 'gray') + + # Default case if no match + return label, 'gray' + + +def add_edges_to_dot(graph, dot): + """Add edges from the graph to the Graphviz object with appropriate labels.""" + for source, target, attributes in graph.edges(data=True): + edge_label = attributes.get('label', '') + if edge_label in ('INPUT_OF', 'DESCRIBES', 'HINT_OF', 'REQUIREMENT_OF'): + dot.edge(source, target, label=edge_label, fontsize="10") + else: + dot.edge(target, source, label=edge_label, fontsize="10") diff --git a/beeflow/common/gdb/graphml_key_updater.py b/beeflow/common/gdb/graphml_key_updater.py new file mode 100644 index 000000000..d18b95481 --- /dev/null +++ b/beeflow/common/gdb/graphml_key_updater.py @@ -0,0 +1,60 @@ +"""Module to make sure all required keys are present.""" + +import xml.etree.ElementTree as ET +import os + +from beeflow.common import paths + +bee_workdir = paths.workdir() +dags_dir = os.path.join(bee_workdir, 'dags') +graphmls_dir = dags_dir + "/graphmls" + +expected_keys = {"id", "name", "state", "class", "type", "value", "source", + "workflow_id", "base_command", "stdout", "stderr", "default", + "prefix", "position", "value_from", "glob"} + +default_key_definitions = { + "id": {"for": "node", "attr.name": "id", "attr.type": "string"}, + "name": {"for": "node", "attr.name": "name", "attr.type": "string"}, + "state": {"for": "node", "attr.name": "state", "attr.type": "string"}, + "class": {"for": "node", "attr.name": "class", "attr.type": "string"}, + "type": {"for": "node", "attr.name": "type", "attr.type": "string"}, + "value": {"for": "node", "attr.name": "value", "attr.type": "string"}, + "source": {"for": "node", "attr.name": "source", "attr.type": "string"}, + "workflow_id": {"for": "node", "attr.name": "workflow_id", "attr.type": "string"}, + "base_command": {"for": "node", "attr.name": "base_command", "attr.type": "string"}, + "stdout": {"for": "node", "attr.name": "stdout", "attr.type": "string"}, + "stderr": {"for": "node", "attr.name": "stderr", "attr.type": "string"}, + "default": {"for": "node", "attr.name": "default", "attr.type": "string"}, + "prefix": {"for": "node", "attr.name": "prefix", "attr.type": "string"}, + "position": {"for": "node", "attr.name": "position", "attr.type": "long"}, + "value_from": {"for": "node", "attr.name": "value_from", "attr.type": "string"}, + "glob": {"for": "node", "attr.name": "glob", "attr.type": "string"}, +} + + +def update_graphml(wf_id): + """Update GraphML file by ensuring required keys are present and updating its structure.""" + short_id = wf_id[:6] + graphml_path = graphmls_dir + "/" + short_id + ".graphml" + # Parse the GraphML file and preserve namespaces + tree = ET.parse(graphml_path) + root = tree.getroot() + + name_space = {'graphml': 'http://graphml.graphdrawing.org/xmlns'} + defined_keys = {key.attrib['id'] for key in root.findall('graphml:key', name_space)} + used_keys = {data.attrib['key'] for data in root.findall('.//graphml:data', name_space)} + + missing_keys = used_keys - defined_keys + + # Insert default key definitions for missing keys + for missing_key in missing_keys: + if missing_key in expected_keys: + default_def = default_key_definitions[missing_key] + key_element = ET.Element(f'{{{name_space["graphml"]}}}key', + id=missing_key, + **default_def) + root.insert(0, key_element) + + # Save the updated GraphML file by overwriting the original one + tree.write(graphml_path, encoding='UTF-8', xml_declaration=True) diff --git a/beeflow/common/gdb/neo4j_cypher.py b/beeflow/common/gdb/neo4j_cypher.py index 6a6cb1f1c..597479c49 100644 --- a/beeflow/common/gdb/neo4j_cypher.py +++ b/beeflow/common/gdb/neo4j_cypher.py @@ -725,3 +725,19 @@ def cleanup(tx): cleanup_query = "MATCH (n) DETACH DELETE n" tx.run(cleanup_query) + + +def export_graphml(tx, wf_id): + """Export BEE workflow as graphml.""" + short_id = wf_id[:6] + export_query = ( + "WITH \"MATCH (n1)-[r]->(n2) " + f"WHERE n1.workflow_id = '{wf_id}' OR n2.workflow_id = '{wf_id}' " + "RETURN r, n1, n2\" AS query " + f"CALL apoc.export.graphml.query(query, '{short_id}.graphml', {{useTypes: true}}) " + "YIELD file, source, format, nodes, relationships, properties, time, rows, batchSize, " + "batches, done, data " + "RETURN file, source, format, nodes, relationships, properties, time, rows, batchSize, " + "batches, done, data" + ) + tx.run(export_query) diff --git a/beeflow/common/gdb/neo4j_driver.py b/beeflow/common/gdb/neo4j_driver.py index 48131a722..c1f444c3c 100644 --- a/beeflow/common/gdb/neo4j_driver.py +++ b/beeflow/common/gdb/neo4j_driver.py @@ -473,6 +473,11 @@ def _write_transaction(self, tx_fun, **kwargs): with self._driver.session() as session: session.write_transaction(tx_fun, **kwargs) + def export_graphml(self, workflow_id): + """Export a BEE workflow as a graphml.""" + with self._driver.session() as session: + session.write_transaction(tx.export_graphml, wf_id=workflow_id) + def _reconstruct_requirements(req_records): """Reconstruct requirements by their records retrieved from Neo4j. diff --git a/beeflow/common/wf_interface.py b/beeflow/common/wf_interface.py index 8fe1054cd..c6b1701cb 100644 --- a/beeflow/common/wf_interface.py +++ b/beeflow/common/wf_interface.py @@ -304,3 +304,7 @@ def workflow_completed(self): :rtype: bool """ return self._gdb_driver.workflow_completed(self._workflow_id) + + def export_graphml(self): + """Export a BEE workflow as a graphml.""" + self._gdb_driver.export_graphml(self._workflow_id) diff --git a/beeflow/wf_manager/resources/wf_utils.py b/beeflow/wf_manager/resources/wf_utils.py index d7b46fb37..efccb2ba5 100644 --- a/beeflow/wf_manager/resources/wf_utils.py +++ b/beeflow/wf_manager/resources/wf_utils.py @@ -8,6 +8,8 @@ from beeflow.common import log as bee_logging from beeflow.common.config_driver import BeeConfig as bc from beeflow.common.gdb import neo4j_driver +from beeflow.common.gdb.generate_graph import generate_viz +from beeflow.common.gdb.graphml_key_updater import update_graphml from beeflow.common.wf_interface import WorkflowInterface from beeflow.common.connection import Connection from beeflow.common import paths @@ -292,6 +294,14 @@ def setup_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, workflow=None, start_workflow(wf_id) +def export_dag(wf_id): + """Export the DAG of the workflow.""" + wfi = get_workflow_interface(wf_id) + wfi.export_graphml() + update_graphml(wf_id) + generate_viz(wf_id) + + def start_workflow(wf_id): """Attempt to start the workflow, returning True if successful.""" db = connect_db(wfm_db, get_db_path()) diff --git a/coverage.svg b/coverage.svg index 012a8497e..a4262d340 100644 --- a/coverage.svg +++ b/coverage.svg @@ -15,7 +15,7 @@ coverage coverage - 70% - 70% + 69% + 69% diff --git a/docs/sphinx/commands.rst b/docs/sphinx/commands.rst index 19ead15af..07ff348b5 100644 --- a/docs/sphinx/commands.rst +++ b/docs/sphinx/commands.rst @@ -102,6 +102,11 @@ Arguments: ``beeflow reexecute``: Reexecute an archived workflow. +Arguments: + WF_ID [required] + +``beeflow dag``: Export a directed acyclic graph (DAG) of a submitted workflow. This command can be run at any point of the workflow. To see the DAG of a workflow before it runs, submit the workflow with the ``--no-start`` flag and then use the dag command. The DAGs are exported to ~/.beeflow/dags. See :ref:`workflow-visualization` for more information. + Arguments: WF_ID [required] diff --git a/docs/sphinx/images/941cd5.png b/docs/sphinx/images/941cd5.png new file mode 100644 index 000000000..c4029f4e1 Binary files /dev/null and b/docs/sphinx/images/941cd5.png differ diff --git a/docs/sphinx/installation.rst b/docs/sphinx/installation.rst index 034eba2a1..cb266ebd0 100644 --- a/docs/sphinx/installation.rst +++ b/docs/sphinx/installation.rst @@ -17,7 +17,7 @@ Requirements: * **Containers**: Two Charliecloud dependency containers are currently required for BEE: one for the Neo4j graph database and another for Redis. The paths to these containers will need to be set in the BEE configuration later, using the ``neo4j_image`` and the ``redis_image`` options respectively. BEE only supports Neo4j 5.x. We are currently using the latest version of Redis supplied on Docker Hub (as of 2023). - For LANL systems, please use the containers supplied by the BEE team: **/usr/projects/BEE/neo4j-5-17.tar.gz**, **/usr/projects/BEE/redis.tar.gz**. + For LANL systems, please use the containers supplied by the BEE team: **/usr/projects/BEE/neo4j.tar.gz**, **/usr/projects/BEE/redis.tar.gz**. For other users, these containers can be pulled from Docker Hub (after following `Installation:`_ below) using ``beeflow core pull-deps``, which will download and report the container paths to be set in the config later. diff --git a/docs/sphinx/visualization.rst b/docs/sphinx/visualization.rst index cd408b419..80cb49987 100644 --- a/docs/sphinx/visualization.rst +++ b/docs/sphinx/visualization.rst @@ -1,56 +1,30 @@ +.. _workflow-visualization: + Workflow Visualization ********************** -BEE includes a simple visualization tool for viewing BEE workflows locally. -This can be installed on a local macOS or Linux-based system using the -JavaScript package manager ``npm``. We plan to make a binary release of this in -the future for ease of use. - -Before attempting to use this tool, you'll need to have BEE running on a -cluster you have SSH access to from your local machine. Submit a workflow and -record the workflow ID, or simply keep track of the ID of an already submitted +BEE includes a simple command for viewing BEE workflows. By using the ``beeflow +dag $ID`` command, you can view the directed acyclic graph (DAG) of any submitted workflow. -**IMPORTANT**: the version of BEE on the cluster must be the same as the -visualization tool installed locally. - -Installation -============ - -First, get an updated clone of the BEE repository, or grab a release tarball -matching the version you have installed on the cluster. Install ``npm`` -following their `installation guide`_. This should be easy to do using your -distro's package manager, or using brew on macOS. - -.. _installation guide: https://docs.npmjs.com/downloading-and-installing-node-js-and-npm - -Making sure that you're in the ``beeflow/enhanced_client`` directory, you can -then install everything with ``npm install``. If your local machine is -connected to a VPN or uses a proxy, you may need to temporarily disable it. -Also take a look at the README in that directory if you need more information. - -Running -======= +Creating DAGs +============= -From the frontend where BEE has been launched, you need to run ``beeflow -metadata ${WF_ID}``, where ``WF_ID`` is the ID of a submitted workflow. You can -safely ignore all the information displayed here, except for the ``bolt_port`` -option which will be needed later. +The dag command can be run at any point of the workflow, and can +be run multiple times. To see the DAG of a workflow before it runs, submit +the workflow with the ``--no-start`` flag and then use the dag command. The +DAGs are exported in PNG format to ~/.beeflow/dags. They follow the naming +convention ``$ID.png`` -On your local machine, given that everything is installed, you can now run -``npm start``, all in the same ``beeflow/enhanced_client`` directory. This will -show a screen that looks like this: +Example DAG +=========== -.. image:: images/bee-viz.png +The DAG below was created by running the dag command while the cat-grep-tar +example workflow was running. -Along the left-hand side you'll see a form containing three fields. Fill in the -the hostname and moniker for the given frontend that BEE is running on (it must -be the exact frontend, otherwise this will fail). Then enter the bolt port -value that should have been saved earlier. Click connect and after a few -seconds the right-hand window should populate with a workflow visual. +.. image:: images/941cd5.png -If any error boxes appear, check your connection and VPN set up. It's possible -that something may be blocking the visual client from connecting to BEE. The -way this currently works is by opening up an SSH tunnel to the frontend on -which BEE is running; if you're able to SSH to that frontend from the same -local machine, then the BEE visualization tool should also be able to. +The orange bubbles are inputs, the blue bubbles are task states, the red +bubbles are tasks, and the green bubbles are outputs. The graph is in a +hierarchical format, meaning that tasks that are higher up in the graph +run before the ones below them. diff --git a/poetry.lock b/poetry.lock index 8b41e933b..dbd07271c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,18 +1,26 @@ +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" optional = false python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] [[package]] name = "amqp" version = "5.2.0" description = "Low-level AMQP client for Python (fork of amqplib)." -category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "amqp-5.2.0-py3-none-any.whl", hash = "sha256:827cb12fb0baa892aad844fd95258143bce4027fdac4fccddbc43330fd281637"}, + {file = "amqp-5.2.0.tar.gz", hash = "sha256:a1ecff425ad063ad42a486c902807d1482311481c8ad95a72694b2975e75f7fd"}, +] [package.dependencies] vine = ">=5.0.0,<6.0.0" @@ -21,9 +29,12 @@ vine = ">=5.0.0,<6.0.0" name = "aniso8601" version = "9.0.1" description = "A library for parsing ISO 8601 strings." -category = "main" optional = false python-versions = "*" +files = [ + {file = "aniso8601-9.0.1-py2.py3-none-any.whl", hash = "sha256:1d2b7ef82963909e93c4f24ce48d4de9e66009a21bf1c1e1c85bdd0812fe412f"}, + {file = "aniso8601-9.0.1.tar.gz", hash = "sha256:72e3117667eedf66951bb2d93f4296a56b94b078a8a95905a052611fb3f1b973"}, +] [package.extras] dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] @@ -32,9 +43,12 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] name = "annotated-types" version = "0.7.0" description = "Reusable constraint 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