DAG Paths

beeflow/client/bee_client.py

@@ -625,9 +625,35 @@ def reexecute(wf_name: str = typer.Argument(..., help='The workflow name'),
 
 
 @app.command()
-def dag(wf_id: str = typer.Argument(..., callback=match_short_id)):
+def dag(wf_id: str = typer.Argument(..., callback=match_short_id),
+        output_dir: pathlib.Path = typer.Argument(...,
+        help='Path to the where the dag output will be'),
+        no_dag_dir: bool = typer.Option(False, '--no-dag-dir',
+        help='do not make a subdirectory within ouput_dir for the dags')):
     """Export a DAG of the workflow to a GraphML file."""
-    wf_utils.export_dag(wf_id)
+    output_dir = output_dir.resolve()
+    # Make sure output_dir is an absolute path and exists
+    output_dir = os.path.expanduser(output_dir)
+    output_dir = os.path.abspath(output_dir)
+    if not os.path.exists(output_dir):
+        error_exit(f"Path for dag directory \"{output_dir}\" doesn't exist")
+
+    # output_dir must be a string
+    output_dir = str(output_dir)
+    # Check if the workflow is archived
+    wf_status = get_wf_status(wf_id)
+    if wf_status == 'Archived':
+        bee_workdir = wf_utils.get_bee_workdir()
+        mount_dir = os.path.join(bee_workdir, 'gdb_mount')
+        graphmls_dir = mount_dir + '/graphmls'
+        typer.secho("Workflow has been archived. All new DAGs will look the same as the one "
+                    "in the archive directory.",
+                    fg=typer.colors.MAGENTA)
+    else:
+        wf_dir = wf_utils.get_workflow_dir(wf_id)
+        graphmls_dir = wf_dir + '/graphmls'
+        os.makedirs(graphmls_dir, exist_ok=True)
+    wf_utils.export_dag(wf_id, output_dir, graphmls_dir, no_dag_dir)
     typer.secho(f"DAG for workflow {_short_id(wf_id)} has been exported successfully.",
                 fg=typer.colors.GREEN)
 

beeflow/common/deps/neo4j_manager.py

@@ -23,8 +23,7 @@
 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"
+graphmls_dir = mount_dir + '/graphmls'
 container_path = container_manager.get_container_dir('neo4j')
 log = bee_logging.setup('neo4j')
 
@@ -61,7 +60,6 @@ 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)
 
 

beeflow/common/gdb/generate_graph.py

@@ -1,21 +1,30 @@
 """Module to make a png of a graph from a graphml file."""
 
 import os
+import shutil
 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):
+def generate_viz(wf_id, output_dir, graphmls_dir, no_dag_dir):
     """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
+
+    if no_dag_dir:
+        dags_dir = output_dir
+    else:
+        dags_dir = output_dir + "/" + short_id + "-dags"
+        os.makedirs(dags_dir, exist_ok=True)
+
+    output_path = dags_dir + "/" + short_id + ".png"
+    if os.path.exists(output_path):
+        i = 1
+        backup_path = f'{dags_dir}/{short_id}_v{i}.png'
+        while os.path.exists(backup_path):
+            i += 1
+            backup_path = f'{dags_dir}/{short_id}_v{i}.png'
+        shutil.copy(output_path, backup_path)
 
     # Load the GraphML file using NetworkX
     graph = nx.read_graphml(graphml_path)
@@ -29,7 +38,7 @@ def generate_viz(wf_id):
 
     # Render the graph and save as PNG
     png_data = dot.pipe(format='png')
-    with open(output_path + ".png", "wb") as png_file:
+    with open(output_path, "wb") as png_file:
         png_file.write(png_data)
 
 

beeflow/common/gdb/graphml_key_updater.py

@@ -2,12 +2,13 @@
 
 import xml.etree.ElementTree as ET
 import os
+import shutil
 
 from beeflow.common import paths
 
 bee_workdir = paths.workdir()
-dags_dir = os.path.join(bee_workdir, 'dags')
-graphmls_dir = dags_dir + "/graphmls"
+mount_dir = os.path.join(bee_workdir, 'gdb_mount')
+gdb_graphmls_dir = mount_dir + '/graphmls'
 
 expected_keys = {"id", "name", "state", "class", "type", "value", "source",
                  "workflow_id", "base_command", "stdout", "stderr", "default",
@@ -33,12 +34,21 @@
 }
 
 
-def update_graphml(wf_id):
+def update_graphml(wf_id, graphmls_dir):
     """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"
+    gdb_graphml_path = gdb_graphmls_dir + "/" + short_id + ".graphml"
+    output_graphml_path = graphmls_dir + "/" + short_id + ".graphml"
+    # Handle making multiple versions of the graphmls without overriding old ones
+    if os.path.exists(output_graphml_path):
+        i = 1
+        backup_path = f'{graphmls_dir}/{short_id}_v{i}.graphml'
+        while os.path.exists(backup_path):
+            i += 1
+            backup_path = f'{graphmls_dir}/{short_id}_v{i}.graphml'
+        shutil.copy(output_graphml_path, backup_path)
     # Parse the GraphML file and preserve namespaces
-    tree = ET.parse(graphml_path)
+    tree = ET.parse(gdb_graphml_path)
     root = tree.getroot()
 
     name_space = {'graphml': 'http://graphml.graphdrawing.org/xmlns'}
@@ -56,5 +66,5 @@ def update_graphml(wf_id):
                                      **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)
+    # Save the updated GraphML file
+    tree.write(output_graphml_path, encoding='UTF-8', xml_declaration=True)

beeflow/common/integration_test.py

@@ -4,6 +4,7 @@
 import os
 import shutil
 import sys
+import time
 import uuid
 import typer
 
@@ -293,6 +294,7 @@ def main(tests = typer.Option(None, '--tests', '-t',  # noqa (conflict on '=' si
          timeout: int = typer.Option(utils.TIMEOUT, '--timeout',
                                      help='workflow timeout in seconds')):
     """Launch the integration tests."""
+    time.sleep(60)
     if show_tests:
         print('INTEGRATION TEST CASES:')
         for test_name, ignore in TEST_RUNNER.test_details():

beeflow/wf_manager/resources/wf_update.py

@@ -26,6 +26,10 @@ def archive_workflow(db, wf_id, final_state=None):
     workflow_dir = wf_utils.get_workflow_dir(wf_id)
     shutil.copyfile(os.path.expanduser("~") + '/.config/beeflow/bee.conf',
                     workflow_dir + '/' + 'bee.conf')
+    # Archive Completed DAG
+    graphmls_dir = workflow_dir + "/graphmls"
+    os.makedirs(graphmls_dir, exist_ok=True)
+    wf_utils.export_dag(wf_id, workflow_dir, graphmls_dir, no_dag_dir=True)
 
     wf_state = f'Archived/{final_state}' if final_state is not None else 'Archived'
     db.workflows.update_workflow_state(wf_id, wf_state)

beeflow/wf_manager/resources/wf_utils.py

@@ -294,12 +294,12 @@ def setup_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, workflow=None,
         start_workflow(wf_id)
 
 
-def export_dag(wf_id):
+def export_dag(wf_id, output_dir, graphmls_dir, no_dag_dir):
     """Export the DAG of the workflow."""
     wfi = get_workflow_interface(wf_id)
     wfi.export_graphml()
-    update_graphml(wf_id)
-    generate_viz(wf_id)
+    update_graphml(wf_id, graphmls_dir)
+    generate_viz(wf_id, output_dir, graphmls_dir, no_dag_dir)
 
 
 def start_workflow(wf_id):

ci/bee_install.sh

@@ -9,8 +9,9 @@ printf "**Setting up BEE containers**\n"
 printf "\n\n"
 mkdir -p $HOME/img
 # Pull the Neo4j container
-ch-image pull neo4j:5.17 || exit 1
-ch-convert -i ch-image -o tar neo4j:5.17 $NEO4J_CONTAINER || exit 1
+chmod +x ./ci/install_apoc_docker
+ch-image build -t apoc_neo4j -f ./ci/install_apoc_docker ./ci || exit 1
+ch-convert -i ch-image -o tar apoc_neo4j $NEO4J_CONTAINER || exit 1
 # Pull the Redis container
 ch-image pull redis || exit 1
 ch-convert -i ch-image -o tar redis $REDIS_CONTAINER || exit 1

ci/deps_install.sh

@@ -7,7 +7,9 @@ sudo apt-get install -y slurmctld slurmd slurmrestd munge python3 python3-venv \
     curl build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev \
     libssl-dev libsqlite3-dev libreadline-dev libffi-dev libbz2-dev \
     libmunge-dev \
-    libyaml-dev # needed for PyYAML
+    libyaml-dev # needed for PyYAML 
+
+sudo apt-get install -y graphviz libgraphviz-dev
 
 # Install most recent Charliecloud
 curl -O -L https://github.com/hpc/charliecloud/releases/download/v${CHARLIECLOUD_VERSION}/charliecloud-${CHARLIECLOUD_VERSION}.tar.gz

ci/install_apoc_docker

@@ -0,0 +1,2 @@
+FROM neo4j:5.17-community 
+RUN cp /var/lib/neo4j/labs/apoc-5.17.0-core.jar /var/lib/neo4j/plugins/apoc-5.17.8-core.jar

docs/sphinx/commands.rst

@@ -105,10 +105,14 @@ Arguments:
 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.
+``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 $OUTPUT_DIR/$WD_ID-dags by default. If the ``no-dag-dir`` flag is specified when the dag command is run, the DAG will be exported to $OUTPUT_DIR. The dag command makes multiple versions of the DAGs. The most recent version is $WF_ID.png and the others are $WD_ID_v1.png, $WF_ID_v2.png ... where v1 is the oldest. See :ref:`workflow-visualization` for more information.
 
 Arguments:
-  WF_ID  [required]
+  - WF_ID  [required]
+  - OUTPUT_DIR, Directory for the output  [required]
+
+Options:
+  ``no-dag-dir``: Do not make a subdirectory within the output_dir for the DAGs.
 
 Generating and Managing Configuration Files
 ===========================================

docs/sphinx/visualization.rst

@@ -4,7 +4,7 @@ Workflow Visualization
 **********************
 
 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
+dag $ID $OUTPUT_DIR`` command, you can view the directed acyclic graph (DAG) of any submitted
 workflow.
 
 Creating DAGs
@@ -13,8 +13,13 @@ Creating DAGs
 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``
+DAGs are exported in PNG format to $OUTPUT_DIR/$WD_ID-dags by default. If the
+``no-dag-dir`` flag is specified when the dag command is run, the DAG will be
+exported to $OUTPUT_DIR. The dag command makes multiple versions of the DAGs. The
+most recent version is $WF_ID.png and the others are $WD_ID_v1.png,
+$WF_ID_v2.png ... where v1 is the oldest. The graphmls used to make the DAGs are saved
+in the workflow archive and are saved with their version number. These graphmls can
+be useful for debugging when there are errors creating the DAGs.
 
 Example DAG
 ===========