diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index e525249d5..ab8408f4d 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -5,11 +5,12 @@ on: push: branches: [main, develop] pull_request: - types: [opened, synchronize, edited] + types: [opened, synchronize, edited, labeled, unlabeled] branches: [main, develop] jobs: docs: + if: ${{ !(contains(github.event.pull_request.labels.*.name, 'WIP (no-ci)')) && !(contains(github.event.pull_request.labels.*.name, 'WIP (lint-only)')) }} name: Build Docs runs-on: ubuntu-latest steps: diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml index f0d5162d7..4dc3a5b07 100644 --- a/.github/workflows/integration.yml +++ b/.github/workflows/integration.yml @@ -14,13 +14,13 @@ env: {} jobs: integration-test: - if: ${{ !(contains(github.event.pull_request.labels.*.name, 'WIP') || contains(github.event.pull_request.labels.*.name, 'lint-only')) }} + if: ${{ !(contains(github.event.pull_request.labels.*.name, 'WIP (no-ci)')) && !(contains(github.event.pull_request.labels.*.name, 'WIP (lint-only)')) }} name: BEE Integration Test strategy: matrix: - batch_scheduler: [Slurm, Flux] + bee_worker: [Slurmrestd, SlurmCommands, Flux] env: - BATCH_SCHEDULER: ${{ matrix.batch_scheduler }} + BEE_WORKER: ${{ matrix.bee_worker }} # Note: Needs to run on 22.04 or later since slurmrestd doesn't seem to be # available on 20.04 runs-on: ubuntu-22.04 diff --git a/.github/workflows/pylama.yml b/.github/workflows/pylama.yml index 831e5187b..3ddd29218 100644 --- a/.github/workflows/pylama.yml +++ b/.github/workflows/pylama.yml @@ -7,11 +7,12 @@ on: push: branches: [main, develop] pull_request: - types: [opened, synchronize, edited] + types: [opened, synchronize, edited, labeled, unlabeled] branches: [main, develop] jobs: pylama: + if: ${{ !(contains(github.event.pull_request.labels.*.name, 'WIP (no-ci)')) }} name: PyLama Lint runs-on: ubuntu-latest steps: diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml index 23d9db533..760e7fa82 100644 --- a/.github/workflows/unit-tests.yml +++ b/.github/workflows/unit-tests.yml @@ -14,11 +14,11 @@ env: {} jobs: integration-test: - if: ${{ !(contains(github.event.pull_request.labels.*.name, 'WIP') || contains(github.event.pull_request.labels.*.name, 'lint-only')) }} + if: ${{ !(contains(github.event.pull_request.labels.*.name, 'WIP (no-ci)')) && !(contains(github.event.pull_request.labels.*.name, 'WIP (lint-only)')) }} name: BEE Unit Tests env: - # Unit tests are only run with Slurm right now - BATCH_SCHEDULER: Slurm + # Unit tests are only run with slurmrestd right now + BEE_WORKER: Slurmrestd # Note: Needs to run on 22.04 or later since slurmrestd doesn't seem to be # available on 20.04 runs-on: ubuntu-22.04 @@ -35,3 +35,36 @@ jobs: run: | . ./ci/env.sh ./ci/unit_tests.sh + + - name: Coverage Badge + if: github.event_name == 'pull_request' + uses: tj-actions/coverage-badge-py@v2 + + - name: Verify Changed Files + if: github.event_name == 'pull_request' + uses: tj-actions/verify-changed-files@v20 + id: verify-changed-files + with: + files: | + *.svg + + - name: Commit files + if: steps.verify-changed-files.outputs.files_changed == 'true' && github.actor != 'github-actions[bot]' && github.event_name == 'pull_request' + run: | + git config --local user.email "github-actions[bot]@users.noreply.github.com" + git config --local user.name "github-actions[bot]" + git add coverage.svg + git commit -m "Updated coverage.svg" + + - name: Fetch latest changes again + if: steps.verify-changed-files.outputs.files_changed == 'true' && github.actor != 'github-actions[bot]' && github.event_name == 'pull_request' + run: | + git fetch origin + git rebase origin/${{ github.event.pull_request.head.ref }} + + - name: Push changes + if: steps.verify-changed-files.outputs.files_changed == 'true' && github.actor != 'github-actions[bot]' && github.event_name == 'pull_request' + uses: ad-m/github-push-action@master + with: + github_token: ${{ secrets.github_token }} + branch: ${{ github.event.pull_request.head.ref }} diff --git a/README.rst b/README.rst index d83f2103d..4962a5d16 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,17 @@ BEE: Build and Execution Environment ************************************ -BEE is a workflow orchestration system designed to build containerized HPC applications and orchestrate workflows across HPC and cloud systems. BEE has adopted the Common Workflow Language (`CWL `_) for specifying workflows. Complex scientific workflows specified by CWL are managed and visualized through a graph database, giving the user the ability to monitor the state of each task in the workflow. BEE runs jobs using the workload scheduler (i.e. Slurm or LSF) on the HPC system that tasks are specified to run on. +Coverage in Develop + +.. image:: https://github.com/lanl/BEE/raw/develop/coverage.svg + :alt: Coverage Badge for develop + +Coverage in Main + +.. image:: https://github.com/lanl/BEE/raw/main/coverage.svg + :alt: Coverage Badge for main + +BEE is a workflow orchestration system designed to build containerized HPC applications and orchestrate workflows across HPC and cloud systems. BEE has adopted the Common Workflow Language (`CWL `_) for specifying workflows. Complex scientific workflows specified by CWL are managed and visualized through a graph database, giving the user the ability to monitor the state of each task in the workflow. BEE runs jobs using the workload scheduler (i.e. Slurm or Flux) on the HPC system that tasks are specified to run on. BEE workflows can be archived for provenance and reproducibility. BEE can orchestrate workflows with containerized applications or those built locally on a system. However, there are advantages to containerizing an application. @@ -46,10 +56,12 @@ Contributors: * Patricia Grubel - `pagrubel `_ * Qiang Guan - `guanxyz `_ * Ragini Gupta - `raginigupta6 `_ +* Leah Howell - `Leahh02 `_ * Andres Quan - `aquan9 `_ * Quincy Wofford - `qwofford `_ * Tim Randles - `trandles-lanl `_ * Jacob Tronge - `jtronge `_ +* Kabir Vats - `kabir-vats `_ Concept and Design Contributors diff --git a/RELEASE.rst b/RELEASE.rst index e894007c8..bbb75caa4 100644 --- a/RELEASE.rst +++ b/RELEASE.rst @@ -18,7 +18,10 @@ Verify all current changes in develop run correctly on nightly tests. 5. Once merged, on github web interface create a release and tag based on main branch that matches the version in pyproject.toml 6. Follow step 2 but uncheck Allow specified actors to bypass and don't forget save -7. Log into your PYPI account and get a token for hpc-beeflow. +7. Log into your PYPI account and get a token for hpc-beeflow via: + + > Your projects > hpc-beeflow > Manage > Settings > Create a token + 8. Finally, on the command line: checkout the main branch and make sure you pull the latest verison Then publish by: @@ -28,7 +31,11 @@ Verify all current changes in develop run correctly on nightly tests. Check the documentation at: `https://lanl.github.io/BEE/ `_ + Also upgrade the pip version in your python or anaconda environment and check the version: + + `` pip install --upgrade pip`` + `` pip install --upgrade hpc-beeflow`` **WARNING**: Once a version is pushed to PyPI, it cannot be undone. You can @@ -36,4 +43,5 @@ Also upgrade the pip version in your python or anaconda environment and check th an update to that same version. 8. After the version is published change the version in develop to a pre-release of the next version - (example new version will be 0.1.x edit pyproject.toml version to be 0.1.xrc1 + (example new version will be 0.1.x edit pyproject.toml version to be 0.1.Xdev + diff --git a/beeflow/client/bee_client.py b/beeflow/client/bee_client.py index 77eedbf0e..1dc03a9bb 100644 --- a/beeflow/client/bee_client.py +++ b/beeflow/client/bee_client.py @@ -11,6 +11,7 @@ import pathlib import shutil import subprocess +import tarfile import tempfile import textwrap import time @@ -18,6 +19,7 @@ import jsonpickle import requests import typer +import yaml from beeflow.common import config_driver from beeflow.common.cli import NaturalOrderGroup @@ -39,6 +41,7 @@ logging.basicConfig(level=logging.WARNING) +logging.getLogger("neo4j").setLevel(logging.WARNING) WORKFLOW_MANAGER = 'bee_wfm/v1/jobs/' @@ -192,7 +195,7 @@ def submit(wf_name: str = typer.Argument(..., help='the workflow name'), # pyli main_cwl: str = typer.Argument(..., help='filename of main CWL (if using CWL tarball), ' + 'path of main CWL (if using CWL directory)'), - yaml: str = typer.Argument(..., + yaml_file: str = typer.Argument(..., help='filename of yaml file (if using CWL tarball), ' + 'path of yaml file (if using CWL directory)'), workdir: pathlib.Path = typer.Argument(..., @@ -206,40 +209,43 @@ def is_parent(parent, path): path = os.path.abspath(path) return os.path.commonpath([parent]) == os.path.commonpath([parent, path]) + wf_path = wf_path.resolve() + workdir = workdir.resolve() + tarball_path = "" if os.path.exists(wf_path): # Check to see if the wf_path is a tarball or a directory. Package if directory if os.path.isdir(wf_path): print("Detected directory instead of packaged workflow. Packaging Directory...") main_cwl_path = pathlib.Path(main_cwl).resolve() - yaml_path = pathlib.Path(yaml).resolve() + yaml_path = pathlib.Path(yaml_file).resolve() if not main_cwl_path.exists(): error_exit(f'Main CWL file {main_cwl} does not exist') if not yaml_path.exists(): - error_exit(f'YAML file {yaml} does not exist') + error_exit(f'YAML file {yaml_file} does not exist') # Packaging in temp dir, after copying alternate cwl_main or yaml file cwl_indir = is_parent(wf_path, main_cwl_path) yaml_indir = is_parent(wf_path, yaml_path) + + # Always create temp dir for the workflow tempdir_path = pathlib.Path(tempfile.mkdtemp()) - if cwl_indir and yaml_indir: - package_path = package(wf_path, tempdir_path) - else: - tempdir_wf_path = pathlib.Path(tempdir_path / wf_path.name) - shutil.copytree(wf_path, tempdir_wf_path, dirs_exist_ok=False) - if not cwl_indir: - shutil.copy2(main_cwl, tempdir_wf_path) - if not yaml_indir: - shutil.copy2(yaml, tempdir_wf_path) - package_path = package(tempdir_wf_path, tempdir_path) + tempdir_wf_path = pathlib.Path(tempdir_path / wf_name) + shutil.copytree(wf_path, tempdir_wf_path, dirs_exist_ok=False) + if not cwl_indir: + shutil.copy2(main_cwl, tempdir_wf_path) + if not yaml_indir: + shutil.copy2(yaml_file, tempdir_wf_path) + package_path = package(tempdir_wf_path, tempdir_path) else: package_path = wf_path + # Untar and parse workflow untar_path = pathlib.Path(tempfile.mkdtemp()) untar_wf_path = unpackage(package_path, untar_path) main_cwl_path = untar_wf_path / pathlib.Path(main_cwl).name - yaml_path = untar_wf_path / pathlib.Path(yaml).name + yaml_path = untar_wf_path / pathlib.Path(yaml_file).name parser = CwlParser() workflow_id = generate_workflow_id() workflow, tasks = parser.parse_workflow(workflow_id, str(main_cwl_path), @@ -259,6 +265,12 @@ def is_parent(parent, path): if not os.path.exists(workdir): error_exit(f"Workflow working directory \"{workdir}\" doesn't exist") + # Make sure the workdir is not in /var or /var/tmp + if os.path.commonpath([os.path.realpath('/tmp'), workdir]) == os.path.realpath('/tmp'): + error_exit("Workflow working directory cannot be in \"/tmp\"") + if os.path.commonpath([os.path.realpath('/var/tmp'), workdir]) == os.path.realpath('/var/tmp'): + error_exit("Workflow working directory cannot be in \"/var/tmp\"") + # TODO: Can all of this information be sent as a file? data = { 'wf_name': wf_name.encode(), @@ -297,16 +309,19 @@ def is_parent(parent, path): # Store provided arguments in text file for future reference wf_dir = wf_utils.get_workflow_dir(wf_id) - sub_wf_dir = wf_dir + "/submit_command_args.txt" + sub_wf_dir = wf_dir + "/submit_command_args.yaml" - f_name = open(sub_wf_dir, "w", encoding="utf-8") - f_name.write(f"wf_name: {wf_name}\n") - f_name.write(f"wf_path: {wf_path}\n") - f_name.write(f"main_cwl: {main_cwl}\n") - f_name.write(f"yaml: {yaml}\n") - f_name.write(f"workdir: {workdir}\n") - f_name.write(f"wf_id: {wf_id}") - f_name.close() + cmd = { + 'wf_name': wf_name, + 'wf_path': str(wf_path), + 'main_cwl': main_cwl, + 'yaml': yaml_file, + 'workdir': workdir, + 'wf_id': wf_id + } + + with open(sub_wf_dir, "w", encoding='utf-8') as command_file: + yaml.dump(cmd, command_file) return wf_id @@ -374,7 +389,7 @@ def remove(wf_id: str = typer.Argument(..., callback=match_short_id)): wf_status = get_wf_status(wf_id) print(f"Workflow Status is {wf_status}") - if wf_status in ('Cancelled', 'Archived', 'Paused'): + if wf_status in ('Cancelled', 'Paused') or 'Archived' in wf_status: verify = f"All stored information for workflow {_short_id(wf_id)} will be removed." verify += "\nContinue to remove? yes(y)/no(n): """ response = input(verify) @@ -450,7 +465,10 @@ def query(wf_id: str = typer.Argument(..., callback=match_short_id)): wf_status = resp.json()['wf_status'] typer.echo(wf_status) for _task_id, task_name, task_state in tasks_status: - typer.echo(f'{task_name}--{task_state}') + if wf_status == 'No Start': + typer.echo(f'{task_name}') + else: + typer.echo(f'{task_name}--{task_state}') logging.info('Query workflow: {resp.text}') return wf_status, tasks_status @@ -511,7 +529,7 @@ def cancel(wf_id: str = typer.Argument(..., callback=match_short_id)): """Cancel a paused or running workflow.""" long_wf_id = wf_id wf_status = get_wf_status(wf_id) - if wf_status in ('Running', 'Paused'): + if wf_status in ('Running', 'Paused', 'No Start'): try: conn = _wfm_conn() resp = conn.delete(_resource(long_wf_id), json={'option': 'cancel'}, timeout=60) @@ -558,6 +576,32 @@ def reexecute(wf_name: str = typer.Argument(..., help='The workflow name'), else: error_exit(f'Workflow tarball {wf_path} cannot be found') + # Make sure the workdir is an absolute path and exists + workdir = os.path.expanduser(workdir) + workdir = os.path.abspath(workdir) + if not os.path.exists(workdir): + error_exit(f"Workflow working directory \"{workdir}\" doesn't exist") + cwl_path = pathlib.Path(tempfile.mkdtemp()) + archive_id = str(wf_path.stem) + with tarfile.open(wf_path) as archive: + archive_cmd = yaml.load(archive.extractfile( + str(pathlib.Path(archive_id) / 'submit_command_args.yaml')).read(), + Loader=yaml.Loader) + + cwl_files = [ + tarinfo for tarinfo in archive.getmembers() + if tarinfo.name.startswith(archive_id + '/cwl_files/') + and tarinfo.isreg() + ] + for path in cwl_files: + path.name = os.path.basename(path.name) + archive.extractall(path=cwl_path, members=cwl_files) + + main_cwl = cwl_path / pathlib.Path(archive_cmd['main_cwl']).name + yaml_file = cwl_path / pathlib.Path(archive_cmd['yaml']).name + + return submit(wf_name, pathlib.Path(cwl_path), main_cwl, yaml_file, pathlib.Path(workdir)) + data = { 'wf_filename': os.path.basename(wf_path).encode(), 'wf_name': wf_name.encode(), @@ -580,6 +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/client/core.py b/beeflow/client/core.py index 74fb71c51..2ea24d912 100644 --- a/beeflow/client/core.py +++ b/beeflow/client/core.py @@ -16,6 +16,7 @@ import shutil import datetime import time +import importlib.metadata import daemon import typer @@ -26,9 +27,9 @@ from beeflow.common import paths from beeflow.wf_manager.resources import wf_utils -from beeflow.common.db import wfm_db -from beeflow.common.db.bdb import connect_db -from beeflow.wf_manager.common import dep_manager +from beeflow.common.deps import container_manager +from beeflow.common.deps import neo4j_manager +from beeflow.common.deps import redis_manager class ComponentManager: @@ -43,7 +44,11 @@ def component(self, name, deps=None): """Return a decorator function to be called.""" def wrap(fn): - """Add the component to the list.""" + """Check to see if any components are disabled.""" + if bc.get('DEFAULT', 'remote_api') is False and 'remote_api' in name: + return + + # Add the component to the list. self.components[name] = { 'fn': fn, 'deps': deps, @@ -188,54 +193,46 @@ def start_scheduler(): return launch_with_gunicorn('beeflow.scheduler.scheduler:create_app()', paths.sched_socket(), stdout=fp, stderr=fp) + @mgr.component('remote_api', ('wf_manager', 'task_manager')) + def start_remote_api(): + """Start the remote API.""" + fp = open_log('remote_api') + return launch_with_gunicorn('beeflow.remote.remote:create_app()', + paths.remote_socket(), stdout=fp, stderr=fp) + @mgr.component('celery', ('redis',)) def celery(): """Start the celery task queue.""" log = open_log('celery') # Setting --pool=solo to avoid preforking multiple processes - return subprocess.Popen(['celery', '-A', 'beeflow.common.celery', 'worker', '--pool=solo'], - stdout=log, stderr=log) + return subprocess.Popen(['celery', '-A', 'beeflow.common.deps.celery_manager', + 'worker', '--pool=solo'], stdout=log, stderr=log) # Run this before daemonizing in order to avoid slow background start - container_path = paths.redis_container() + # container_path = paths.redis_container() # If it exists, we assume that it actually has a valid container - if not os.path.exists(container_path): + # if not os.path.exists(container_path): + # print('Unpacking Redis image...') + # subprocess.check_call(['ch-convert', '-i', 'tar', '-o', 'dir', + # bc.get('DEFAULT', 'redis_image'), container_path]) + if not container_manager.check_container_dir('redis'): print('Unpacking Redis image...') - subprocess.check_call(['ch-convert', '-i', 'tar', '-o', 'dir', - bc.get('DEFAULT', 'redis_image'), container_path]) + container_manager.create_image('redis') + + if not container_manager.check_container_dir('neo4j'): + print('Unpacking Neo4j image...') + container_manager.create_image('neo4j') + + @mgr.component('neo4j-database', ('wf_manager',)) + def start_neo4j(): + """Start the neo4j graph database.""" + return neo4j_manager.start() @mgr.component('redis', ()) - def redis(): + def start_redis(): """Start redis.""" - data_dir = 'data' - os.makedirs(os.path.join(paths.redis_root(), data_dir), exist_ok=True) - conf_name = 'redis.conf' - container_path = paths.redis_container() - # Dump the config - conf_path = os.path.join(paths.redis_root(), conf_name) - if not os.path.exists(conf_path): - with open(conf_path, 'w', encoding='utf-8') as fp: - # Don't listen on TCP - print('port 0', file=fp) - print('dir', os.path.join('/mnt', data_dir), file=fp) - print('maxmemory 2mb', file=fp) - print('unixsocket', os.path.join('/mnt', paths.redis_sock_fname()), file=fp) - print('unixsocketperm 700', file=fp) - cmd = [ - 'ch-run', - f'--bind={paths.redis_root()}:/mnt', - container_path, - 'redis-server', - '/mnt/redis.conf', - ] log = open_log('redis') - # Ran into a strange "Failed to configure LOCALE for invalid locale name." - # from Redis, so setting LANG=C. This could have consequences for UTF-8 - # strings. - env = dict(os.environ) - env['LANG'] = 'C' - env['LC_ALL'] = 'C' - return subprocess.Popen(cmd, env=env, stdout=log, stderr=log) + return redis_manager.start(log) # Workflow manager and task manager need to be opened with PIPE for their stdout/stderr if need_slurmrestd(): @@ -246,9 +243,10 @@ def start_slurm_restd(): slurmrestd_log = '/'.join([bee_workdir, 'logs', 'restd.log']) openapi_version = bc.get('slurm', 'openapi_version') slurm_args = f'-s openapi/{openapi_version}' + # The following adds the db plugin we opted not to use for now + # slurm_args = f'-s openapi/{openapi_version},openapi/db{openapi_version}' slurm_socket = paths.slurm_socket() subprocess.run(['rm', '-f', slurm_socket], check=True) - # log.info("Attempting to open socket: {}".format(slurm_socket)) fp = open(slurmrestd_log, 'w', encoding='utf-8') # noqa cmd = ['slurmrestd'] cmd.extend(slurm_args.split()) @@ -407,7 +405,9 @@ def start(foreground: bool = typer.Option(False, '--foreground', '-F', # It's already running, so print an error and exit warn(f'Beeflow appears to be running. Check the beeflow log: "{beeflow_log}"') sys.exit(1) - print('Starting beeflow...') + + version = importlib.metadata.version("hpc-beeflow") + print(f'Starting beeflow {version}...') if not foreground: print('Run `beeflow core status` for more information.') # Create the log path if it doesn't exist yet @@ -437,19 +437,38 @@ def status(): print(f'{comp} ... {stat}') +@app.command() +def info(): + """Get information about beeflow's installation.""" + version = importlib.metadata.version("hpc-beeflow") + print(f"Beeflow version: {version}") + print(f"bee_workflow directory: {paths.workdir()}") + print(f"Log path: {paths.log_path()}") + + @app.command() def stop(query='yes'): """Stop the current running beeflow daemon.""" - if query == 'yes': + # Check workflow states; warn if there are active states, pause running workflows + workflow_list = bee_client.get_wf_list() + concern_states = {'Running', 'Initializing', 'Waiting'} + concern = {item for row in workflow_list for item in row}.intersection(concern_states) + # For the interactive case + if query == 'yes' and concern: ans = input(""" - ** Please ensure all workflows are complete before stopping beeflow. ** - ** Check the status of workflows by running 'beeflow list'. ** + ** There are running workflows. ** + ** Running workflows will be paused. ** Are you sure you want to kill beeflow components? [y/n] """) else: ans = 'y' if ans.lower() != 'y': return + # Pause running or waiting workflows + workflow_list = bee_client.get_wf_list() + for _name, wf_id, state in workflow_list: + if state in {'Running', 'Waiting'}: + bee_client.pause(wf_id) resp = cli_connection.send(paths.beeflow_socket(), {'type': 'quit'}) if resp is None: beeflow_log = paths.log_fname('beeflow') @@ -459,27 +478,10 @@ def stop(query='yes'): sys.exit(1) # As long as it returned something, we should be good beeflow_log = paths.log_fname('beeflow') - if query == "no": + if query == "yes": print(f'Beeflow has stopped. Check the log at "{beeflow_log}".') -def kill_active_workflows(active_states, workflow_list): - """Kill workflows with active states.""" - db_path = wf_utils.get_db_path() - db = connect_db(wfm_db, db_path) - success = True - for name, wf_id, state in workflow_list: - if state in active_states: - pid = db.workflows.get_gdb_pid(wf_id) - if pid > 0: - dep_manager.kill_gdb(pid) - else: - # Failure most likely caused by an Initializing workflow. - print(f"No process for {name}, {wf_id}, {state}.") - success = False - return success - - def archive_dir(dir_to_archive): """Archive directories for archive flag in reset.""" archive_dirs = ['logs', 'container_archive', 'archives', 'workflows'] @@ -547,9 +549,6 @@ def reset(archive: bool = typer.Option(False, '--archive', '-a', # Exit out if the user didn't really mean to do a reset sys.exit() elif absolutely_sure in ("y", "yes"): - # First stop all active workflow processes - workflow_list = bee_client.get_wf_list() - kill_active_workflows(active_states, workflow_list) # Stop all of the beeflow processes stop("quiet") print("Beeflow is shutting down.") @@ -590,7 +589,7 @@ 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() diff --git a/beeflow/common/config_driver.py b/beeflow/common/config_driver.py index f73c7a6b6..3b26432a3 100644 --- a/beeflow/common/config_driver.py +++ b/beeflow/common/config_driver.py @@ -225,50 +225,63 @@ def filepath_completion_input(*pargs, **kwargs): DEFAULT_SCHED_PORT = 5100 + OFFSET DEFAULT_BEE_WORKDIR = join_path(HOME_DIR, '.beeflow') +DEFAULT_BEE_DROPPOINT = join_path(HOME_DIR, '.beeflow/droppoint') USER = getpass.getuser() # Create the validator VALIDATOR = ConfigValidator('BEE configuration file and validation information.') VALIDATOR.section('DEFAULT', info='Default bee.conf configuration section.') + VALIDATOR.option('DEFAULT', 'bee_workdir', info='main BEE workdir', - attrs={'default': DEFAULT_BEE_WORKDIR}, validator=validation.make_dir) + default=DEFAULT_BEE_WORKDIR, validator=validation.make_dir) + +VALIDATOR.option('DEFAULT', 'bee_droppoint', info='BEE remote workflow drop point', + default=DEFAULT_BEE_DROPPOINT, validator=validation.make_dir) + +VALIDATOR.option('DEFAULT', 'remote_api', info='BEE remote REST API activation', + default=False, validator=validation.bool_) + +VALIDATOR.option('DEFAULT', 'remote_api_port', info='BEE remote REST API port', + default=7777, validator=int) + VALIDATOR.option('DEFAULT', 'workload_scheduler', choices=('Slurm', 'LSF', 'Flux', 'Simple'), info='backend workload scheduler to interact with ') -VALIDATOR.option('DEFAULT', 'use_archive', validator=validation.bool_, attrs={'default': True}, - info='use the BEE archiving functinality') + +VALIDATOR.option('DEFAULT', 'delete_completed_workflow_dirs', validator=validation.bool_, + default=True, info='delete workflow directory for completed jobs') + VALIDATOR.option('DEFAULT', 'neo4j_image', validator=validation.file_, info='neo4j container image', - attrs={'input': filepath_completion_input}) + input_fn=filepath_completion_input) + VALIDATOR.option('DEFAULT', 'redis_image', validator=validation.file_, info='redis container image', - attrs={'input': filepath_completion_input}) + input_fn=filepath_completion_input) + VALIDATOR.option('DEFAULT', 'max_restarts', validator=int, - attrs={'default': 3}, + default=3, info='max number of times beeflow will restart a component on failure') + # Workflow Manager VALIDATOR.section('workflow_manager', info='Workflow manager section.') # Task manager VALIDATOR.section('task_manager', info='Task manager configuration and config of container to use.') -VALIDATOR.option('task_manager', 'container_runtime', attrs={'default': 'Charliecloud'}, +VALIDATOR.option('task_manager', 'container_runtime', default='Charliecloud', choices=('Charliecloud', 'Singularity'), info='container runtime to use for configuration') -VALIDATOR.option('task_manager', 'runner_opts', attrs={'default': ''}, +VALIDATOR.option('task_manager', 'runner_opts', default='', info='special runner options to pass to the runner opts') -VALIDATOR.option('task_manager', 'background_interval', attrs={'default': 5}, +VALIDATOR.option('task_manager', 'background_interval', default=5, validator=int, info='interval at which the task manager processes queues and updates states') -# Note: The special attrs keyword can include anything. One use case is for -# storing a special 'init' function that can be used to initialize the -# parameter when a user is generating a new configuration. - # Charliecloud (depends on task_manager::container_runtime == Charliecloud) VALIDATOR.section('charliecloud', info='Charliecloud configuration section.', depends_on=('task_manager', 'container_runtime', 'Charliecloud')) -VALIDATOR.option('charliecloud', 'image_mntdir', attrs={'default': join_path('/tmp', USER)}, +VALIDATOR.option('charliecloud', 'image_mntdir', default=join_path('/tmp', USER), info='Charliecloud mount directory', validator=validation.make_dir) # General job requirements -VALIDATOR.section('job', info='General job requirements') +VALIDATOR.section('job', info='General job requirements.') VALIDATOR.option('job', 'default_account', validator=lambda val: val.strip(), info='default account to launch jobs with (leave blank if none)') VALIDATOR.option('job', 'default_time_limit', validator=validation.time_limit, @@ -287,53 +300,53 @@ def validate_chrun_opts(opts): return opts -VALIDATOR.option('charliecloud', 'chrun_opts', attrs={'default': '--home'}, +VALIDATOR.option('charliecloud', 'chrun_opts', default='--home', validator=validate_chrun_opts, info='extra options to pass to ch-run') -VALIDATOR.option('charliecloud', 'setup', attrs={'default': ''}, +VALIDATOR.option('charliecloud', 'setup', default='', info='extra Charliecloud setup to put in a job script') # Graph Database VALIDATOR.section('graphdb', info='Main graph database configuration section.') -VALIDATOR.option('graphdb', 'hostname', attrs={'default': 'localhost'}, +VALIDATOR.option('graphdb', 'hostname', default='localhost', info='hostname of database') -VALIDATOR.option('graphdb', 'dbpass', attrs={'default': 'password'}, info='password for database') -VALIDATOR.option('graphdb', 'bolt_port', attrs={'default': DEFAULT_BOLT_PORT}, validator=int, +VALIDATOR.option('graphdb', 'dbpass', default='password', info='password for database') +VALIDATOR.option('graphdb', 'bolt_port', default=DEFAULT_BOLT_PORT, validator=int, info='port used for the BOLT API') -VALIDATOR.option('graphdb', 'http_port', attrs={'default': DEFAULT_HTTP_PORT}, validator=int, +VALIDATOR.option('graphdb', 'http_port', default=DEFAULT_HTTP_PORT, validator=int, info='HTTP port used for the graph database') -VALIDATOR.option('graphdb', 'https_port', attrs={'default': DEFAULT_HTTPS_PORT}, +VALIDATOR.option('graphdb', 'https_port', default=DEFAULT_HTTPS_PORT, info='HTTPS port used for the graph database') -VALIDATOR.option('graphdb', 'gdb_image_mntdir', attrs={'default': join_path('/tmp', USER)}, +VALIDATOR.option('graphdb', 'gdb_image_mntdir', default=join_path('/tmp', USER), info='graph database image mount directory', validator=validation.make_dir) -VALIDATOR.option('graphdb', 'sleep_time', validator=int, attrs={'default': 10}, +VALIDATOR.option('graphdb', 'sleep_time', validator=int, default=1, info='how long to wait for the graph database to come up (this can take a while, ' 'depending on the system)') # Builder VALIDATOR.section('builder', info='General builder configuration section.') -VALIDATOR.option('builder', 'deployed_image_root', attrs={'default': '/tmp'}, +VALIDATOR.option('builder', 'deployed_image_root', default='/tmp', info='where to deploy container images', validator=validation.make_dir) -VALIDATOR.option('builder', 'container_output_path', attrs={'default': '/tmp'}, +VALIDATOR.option('builder', 'container_output_path', default='/tmp', info='container output path', validator=validation.make_dir) VALIDATOR.option('builder', 'container_archive', - attrs={'default': join_path(DEFAULT_BEE_WORKDIR, 'container_archive')}, + default=join_path(DEFAULT_BEE_WORKDIR, 'container_archive'), info='container archive location') -VALIDATOR.option('builder', 'container_type', attrs={'default': 'charliecloud'}, +VALIDATOR.option('builder', 'container_type', default='charliecloud', info='container type to use') # Slurmrestd (depends on DEFAULT:workload_scheduler == Slurm) VALIDATOR.section('slurm', info='Configuration section for Slurm.', depends_on=('DEFAULT', 'workload_scheduler', 'Slurm')) VALIDATOR.option('slurm', 'use_commands', validator=validation.bool_, - attrs={'default': shutil.which('slurmrestd') is None}, + default=(shutil.which('slurmrestd') is None), info='if set, use slurm cli commands instead of slurmrestd') DEFAULT_SLURMRESTD_SOCK = join_path('/tmp', f'slurm_{USER}_{random.randint(1, 10000)}.sock') -VALIDATOR.option('slurm', 'openapi_version', attrs={'default': 'v0.0.37'}, +VALIDATOR.option('slurm', 'openapi_version', default='v0.0.39', info='openapi version to use for slurmrestd') # Scheduler VALIDATOR.section('scheduler', info='Scheduler configuration section.') SCHEDULER_ALGORITHMS = ('fcfs', 'backfill', 'sjf') -VALIDATOR.option('scheduler', 'algorithm', attrs={'default': 'fcfs'}, choices=SCHEDULER_ALGORITHMS, +VALIDATOR.option('scheduler', 'algorithm', default='fcfs', choices=SCHEDULER_ALGORITHMS, info='scheduling algorithm to use') -VALIDATOR.option('scheduler', 'default_algorithm', attrs={'default': 'fcfs'}, +VALIDATOR.option('scheduler', 'default_algorithm', default='fcfs', choices=SCHEDULER_ALGORITHMS, info=('default algorithm to use')) @@ -384,12 +397,9 @@ def choose_values(self): printed = True # Check for a default value - if option.attrs is not None and 'default' in option.attrs: - default = option.attrs['default'] - if option.attrs is not None and 'init' in option.attrs: - value = option.attrs['init'](default, self.sections) - else: - value = option.validate(default) + if option.default is not None: + default = option.default + value = option.validate(default) print(f'Setting option "{opt_name}" to default value "{value}".') print() self.sections[sec_name][opt_name] = value @@ -405,18 +415,14 @@ def choose_values(self): def _input_loop(self, opt_name, option): """Run the input-validation loop.""" # Check if there's a special input function (this allows for tab completion) - inp = (option.attrs['input'] if option.attrs is not None - and 'input' in option.attrs else input) + input_fn = option.input_fn if option.input_fn is not None else input # Start of input loop value = None while value is None: print_wrap(f'{opt_name} - {option.info}') if option.choices is not None: print(f'(allowed values: {",".join(option.choices)})') - value = inp(f'{opt_name}: ') - # Call the init function if there is one - if option.attrs is not None and 'init' in option.attrs: - option.attrs['init'](value, self.sections) + value = input_fn(f'{opt_name}: ') # Validate the input try: option.validate(value) @@ -479,17 +485,18 @@ def info(): print() for sec_name, section in VALIDATOR.sections: print(f'## {sec_name}') + print() + print_wrap(section.info) if section.depends_on is not None: - print() deps = section.depends_on - print_wrap(f'*only required if {deps[0]}::{deps[1]} == "{deps[2]}"*') - print() - print_wrap(f'{section.info}') + print() + print_wrap(f'Section required if {deps[0]}::{deps[1]} == "{deps[2]}".') print() + print('Options:') for opt_name, option in VALIDATOR.options(sec_name): print_wrap(f'* {opt_name} - {option.info}', ' ') if option.choices is not None: - print(f'\t* allowed values: {",".join(option.choices)}') + print(f' * allowed values: {",".join(option.choices)}') print() diff --git a/beeflow/common/config_validator.py b/beeflow/common/config_validator.py index 17f2cb3b7..9f4036fbc 100644 --- a/beeflow/common/config_validator.py +++ b/beeflow/common/config_validator.py @@ -1,4 +1,8 @@ -"""Configuration validation.""" +"""Config validation code.""" + +from beeflow.common import log as bee_logging + +log = bee_logging.setup(__name__) class ConfigError(Exception): @@ -18,43 +22,69 @@ def __init__(self, description): def validate(self, conf): """Validate a config and return a new config with defaults and values converted.""" new_conf = {} - # first validate each option + errors = [] + + self._validate_existing_options(conf, new_conf, errors) + self._check_required_options(conf, new_conf, errors) + + # Bundle up all the errors into one exception + if errors: + message = ['Config validation failed:\n'] + message.extend(f' * {error}\n' for error in errors) + raise ConfigError(''.join(message)) + + return new_conf + + def _validate_existing_options(self, conf, new_conf, errors): + """Validate existing options within the config.""" + # First validate each option for sec_name in conf: - new_conf[sec_name] = {} section = conf[sec_name] if sec_name not in self._sections: - raise ValueError(f'section "{sec_name}" is not defined') - # check that this section is valid in this context + log.warning(f'config contains invalid section "{sec_name}"') + continue + new_conf[sec_name] = {} + # Check that this section is valid in this context dep = self._sections[sec_name].depends_on if not self._validate_section(conf, depends_on=dep): - raise ValueError( + errors.append( f"section '{sec_name}' requires that {dep[0]}::{dep[1]} == '{dep[2]}'" ) - # validate each option + continue + # Validate each option for opt_name in section: key = (sec_name, opt_name) if key not in self._options: - raise ValueError( - f"option '{opt_name}' in section '{sec_name}' is not defined" - ) + log.warning(f"option {sec_name}::{opt_name} is not a valid option") + continue option = self._options[key] try: new_conf[sec_name][opt_name] = option.validate(section[opt_name]) except ValueError as err: - raise ValueError( - f'{sec_name}::{opt_name}: {err.args[0]}' - ) from None - # then check required options - for key in self._options: - if not self._validate_section(conf, self._sections[key[0]].depends_on): - # skip invalid sections + errors.append(f'{sec_name}::{opt_name}: {err.args[0]}') + + def _check_required_options(self, conf, new_conf, errors): + """Check for required options and set defaults as necessary.""" + # Then check required options + for sec_name, opt_name in self._options: + key = (sec_name, opt_name) + if not self._validate_section(conf, self._sections[sec_name].depends_on): + # Skip invalid sections continue - if key[0] not in conf or key[1] not in conf[key[0]]: - raise ValueError( - f"option '{key[1]}' in section '{key[0]}' is required but has not been set" - ) - - return new_conf + if sec_name not in conf or opt_name not in conf[sec_name]: + default = self._options[key].default + if default is None: + errors.append( + f'option {sec_name}::{opt_name} is required but has not been set' + ) + continue + # Set the default, but warn the user + log.warning(f'option {sec_name}::{opt_name} is missing, setting to default ' + f'"{default}"; please check that that is correct and update the ' + 'config') + if sec_name not in new_conf: + new_conf[sec_name] = {} + new_conf[sec_name][opt_name] = default def _validate_section(self, conf, depends_on): """Ensure that this section is valid in this context (check depends relations).""" @@ -62,7 +92,7 @@ def _validate_section(self, conf, depends_on): return True if depends_on[0] not in conf or depends_on[1] not in conf[depends_on[0]]: return False - # value must match for the section to be valid + # Value must match for the section to be valid return conf[depends_on[0]][depends_on[1]] == depends_on[2] def is_section_valid(self, cur_conf, sec_name): @@ -78,7 +108,7 @@ def section(self, sec_name, info, depends_on=None): if sec_name in self._sections: raise ConfigError(f"section '{sec_name}' has already been defined") self._sections[sec_name] = ConfigSection(info, depends_on=depends_on) - # save insertion order + # Save insertion order self._section_order.append(sec_name) def option(self, sec_name, opt_name, *args, **kwargs): @@ -87,9 +117,7 @@ def option(self, sec_name, opt_name, *args, **kwargs): raise ConfigError(f"section '{sec_name}' has not been defined") key = (sec_name, opt_name) if key in self._options: - raise ConfigError( - f"option '{opt_name}' in section '{sec_name}' has already been defined" - ) + raise ConfigError(f'option {sec_name}::{opt_name} has already been defined') try: self._options[key] = ConfigOption(*args, **kwargs) except ConfigError as err: @@ -132,12 +160,14 @@ def __init__(self, info, depends_on=None): class ConfigOption: """Config option/validation class.""" - def __init__(self, info, validator=str, choices=None, attrs=None): + def __init__(self, info, validator=str, choices=None, default=None, input_fn=None): """Construct the config option class.""" self.info = info self.choices = choices - # attrs is designed to hold any extra attribute that could be useful - self.attrs = attrs + # Default value, if None the option is required + self.default = default + # Function used to set the option from user input at config generation time + self.input_fn = input_fn self._validator = validator def validate(self, value): @@ -147,5 +177,3 @@ def validate(self, value): raise ValueError(f"value must be one of {self.choices}; found '{value}'") return value return self._validator(value) -# Ignore C901: "'ConfigValidator.validate' is too complex" - this function is under 40 LOC -# pylama:ignore=C901 diff --git a/beeflow/common/cwl/cwl.py b/beeflow/common/cwl/cwl.py new file mode 100644 index 000000000..9fcd1a4fb --- /dev/null +++ b/beeflow/common/cwl/cwl.py @@ -0,0 +1,545 @@ +"""Create and manage CWL files.""" +from dataclasses import dataclass +import yaml + + +@dataclass +class Header: + """Represents a CWL header.""" + + class_type: str = "Workflow" + cwl_version: str = "v1.0" + + def dump(self): + """Dump CWL header dictionary.""" + return {'class': self.class_type, 'cwlVersion': self.cwl_version} + + def __repr__(self): + """Return CWL header as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class Input: + """The base input class. Used by CWLInput and RunInput. + + CWLInput has an input_default while RunInput has an inputBinding + and RunInput has an inputBinding + """ + + input_name: str + input_type: str + + def dump(self): + """Dump returns dictionary that will be used by pyyaml dump.""" + input_yaml = {self.input_name: self.input_type} + return input_yaml + + def __repr__(self): + """Representation of an input. + + input_name: input_type + """ + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class CWLInput(Input): + """Represents a CWL input as opposed to a Run input.""" + + value: str + + +@dataclass +class InputBinding: + """Represents a CWL input binding.""" + + prefix: str = None + position: int = None + + def dump(self): + """Dump returns dictionary that will be used by pyyaml dump.""" + binding_yaml = {'inputBinding': {}} + if self.position: + binding_yaml['inputBinding']['position'] = self.position + if self.prefix: + binding_yaml['inputBinding']['prefix'] = self.prefix + return binding_yaml + + def __repr__(self): + """Representation of an input. + + input_name: input_type + """ + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class RunInput(Input): + """Represents a Run input as opposed to a CWL input. + + InputBinding can either be: + prefix: <-j> or empty {} + """ + + input_binding: InputBinding + # For now source will just be a string but might make it a type later + source: str = None + + def dump(self): + """Dump returns dictionary that will be used by pyyaml dump.""" + inputs_dumps = [{'type': self.input_type}, + self.input_binding.dump()] + inputs_dict = {} + for dump in inputs_dumps: + inputs_dict.update(dump) + inputs_yaml = {self.input_name: inputs_dict} + return inputs_yaml + + def __repr__(self): + """Representation of an input. + + input_name: input_type + """ + return yaml.dump(self.dump(), sort_keys=False) + + +class Inputs: + """Represents CWL or Run inputs for a workflow.""" + + def __init__(self, inputs=None): + """Initialize inputs.""" + self.inputs = inputs + + def dump(self): + """Return CWL input dict.""" + inputs_dumps = [i.dump() for i in self.inputs] + inputs_dict = {} + for input_dump in inputs_dumps: + inputs_dict.update(input_dump) + input_yaml = {'inputs': inputs_dict} + return input_yaml + + def __add__(self, adder_inputs): + """Add inputs.""" + new_inputs = self.inputs + adder_inputs.inputs + return Inputs(new_inputs) + + def __repr__(self): + """Return Inputs as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +class CWLInputs(Inputs): + """CWLInputs is different just so we can generate the YAML file.""" + + def generate_yaml_inputs(self): + """Return a dictionary that will be used to create job yaml file.""" + yaml_inputs = {} + for i in self.inputs: + yaml_inputs[i.input_name] = i.value + return yaml_inputs + + +@dataclass +class Output: + """Represents a CWL input.""" + + output_name: str + output_type: str + + def dump(self): + """Dump the output to a dictionary. + + output_name: + type: output_type + """ + output = {self.output_name: {'type': self.output_type}} + return output + + def __repr__(self): + """Return Output as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class OutputBinding: + """Represents a CWL input binding.""" + + prefix: str = None + position: int = None + + def dump(self): + """Dump returns dictionary that will be used by pyyaml dump.""" + binding_yaml = {'outputBinding': {}} + if self.position: + binding_yaml['outputBinding']['position'] = self.position + if self.prefix: + binding_yaml['outputBinding']['prefix'] = self.prefix + return binding_yaml + + def __repr__(self): + """Representation of an output. + + output_name: output_type + """ + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class RunOutput(Output): + """Represents a Run output as opposed to a CWL output. + + InputBinding can either be: + prefix: <-j> + {} + """ + + output_binding: OutputBinding = None + + def dump(self): + """Dump returns dictionary that will be used by pyyaml dump.""" + if not self.output_binding: + return super().dump() + outputs_dumps = [{'type': self.output_type}, + self.output_binding.dump()] + outputs_dict = {} + for dump in outputs_dumps: + outputs_dict.update(dump) + inputs_yaml = {self.output_name: outputs_dict} + return inputs_yaml + + def __repr__(self): + """Representation of an input. + + input_name: input_type + """ + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class CWLOutput(Output): + """Represents a CWL input.""" + + output_source: str = None + + def dump(self): + """Dump the output to a dictionary. + + output_name: + type: output_type + outputSource: output_src/output_name + """ + if self.output_source is not None: + output = {self.output_name: {'type': self.output_type, + 'outputSource': self.output_source}} + else: + output = {self.output_name: {'type': self.output_type}} + return output + + def __repr__(self): + """Return CWLOutput as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +class Outputs: + """Represents outputs for a workflow.""" + + def __init__(self, outputs): + """Initialize outputs.""" + self.outputs = outputs + + def dump(self): + """Dump workflow inputs to a dictionary.""" + outputs_dumps = [i.dump() for i in self.outputs] + outputs_dict = {k: v for d in outputs_dumps for k, v in d.items()} + output_yaml = {'outputs': outputs_dict} + return output_yaml + + def __add__(self, adder_outputs): + """Add outputs.""" + new_outputs = self.outputs + adder_outputs.outputs + return Outputs(new_outputs) + + def __repr__(self): + """Return Outputs as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class DockerRequirement: + """Defines docker requirement.""" + + docker_pull: str = None + docker_file: str = None + copy_container: str = None + use_container: str = None + container_name: str = None + force_type: str = None + + def dump(self): + """Dump docker requirement to a dictionary.""" + docker_dump = {'DockerRequirement': {}} + if self.docker_pull: + docker_dump['DockerRequirement']['dockerPull'] = self.docker_pull + if self.docker_file: + docker_dump['DockerRequirement']['dockerFile'] = self.docker_file + if self.copy_container: + docker_dump['DockerRequirement']['beeflow:copyContainer'] = self.copy_container + if self.use_container: + docker_dump['DockerRequirement']['beeflow:useContainer'] = self.use_container + if self.container_name: + docker_dump['DockerRequirement']['beeflow:containerName'] = self.container_name + if self.force_type: + docker_dump['DockerRequirement']['beeflow:force=Type'] = self.force_type + return docker_dump + + def __repr__(self): + """Return DockerRequirement as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class MPIRequirement: + """Represents a beeflow custom MPI requirement.""" + + nodes: int = None + ntasks: int = None + + def dump(self): + """Dump MPI requirement to dictionary.""" + mpi_dump = {'beeflow:MPIRequirement': {}} + if self.nodes: + mpi_dump['beeflow:MPIRequirement']['nodes'] = self.nodes + if self.ntasks: + mpi_dump['beeflow:MPIRequirement']['ntasks'] = self.ntasks + return mpi_dump + + def __repr__(self): + """Return MPIRequirement as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class CheckpointRequirement: + """Represents a beeflow checkpoint requirement.""" + + file_path: str + container_path: str + file_regex: str + restart_parameters: str + num_tries: int + enabled: bool = True + + def dump(self): + """Dump beeflow requirement to a dictionary.""" + req_name = 'beeflow:CheckpointRequirement' + checkpoint_dump = {req_name: {}} + checkpoint_dump[req_name]['enabled'] = self.enabled + checkpoint_dump[req_name]['file_path'] = self.file_path + checkpoint_dump[req_name]['container_path'] = self.container_path + checkpoint_dump[req_name]['file_regex'] = self.file_regex + checkpoint_dump[req_name]['restart_parameters'] = self.restart_parameters + checkpoint_dump[req_name]['num_tries'] = self.enabled + return req_name + + def __repr__(self): + """Return CheckpointRequirement as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class ScriptRequirement: + """Represents a beeflow custom pre/post script requirement.""" + + pre_script: str = None + post_script: str = None + enabled: bool = True + shell: str = "/bin/bash" + + def dump(self): + """Dump script requirement to a dcitionary.""" + key = 'beeflow:ScriptRequirement' + script_dump = {key: {}} + if self.pre_script: + script_dump[key]['pre_script'] = self.pre_script + if self.post_script: + script_dump[key]['post_script'] = self.post_script + script_dump[key]['enabled'] = self.enabled + script_dump[key]['shell'] = self.shell + return script_dump + + def __repr__(self): + """Return ScriptRequirement as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +@dataclass +class Hints: + """Holds all the hints for a CWL workflow.""" + + mpi_requirement: MPIRequirement = None + docker_requirement: DockerRequirement = None + script_requirement: ScriptRequirement = None + checkpoint_requirement: CheckpointRequirement = None + + def dump(self): + """Dump hints to a dictionary.""" + hints_dump = {'hints': {}} + if self.mpi_requirement: + hints_dump['hints'].update(self.mpi_requirement.dump()) + if self.docker_requirement: + hints_dump['hints'].update(self.docker_requirement.dump()) + if self.script_requirement: + hints_dump['hints'].update(self.script_requirement.dump()) + if self.checkpoint_requirement: + hints_dump['hints'].update(self.checkpoint_requirement.dump()) + return hints_dump + + def __repr__(self): + """Return Hint as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +class Run: + """Represents a run section for a CWL workflow. + + Each task in a CWL workflow has a run section which can either be + external to the main CWL file in its own CWL or be embedded directly + into the main CWL file. For now, we're just embedding this directly + into the main CWL file for ease of use, but might add an external option + later. + """ + + def __init__(self, base_command, inputs, outputs, stdout, stderr=None): + """Initialize Run.""" + # This is implicit since we only support CommandLineTool steps atm + self.run_class = 'CommandLineTool' + self.base_command = base_command + self.inputs = inputs + self.outputs = outputs + self.stdout = stdout + self.stderr = stderr + + def dump(self): + """Dump run section into a dictionary.""" + run_dump = {'run': {}} + run_dump['run']['class'] = self.run_class + run_dump['run']['baseCommand'] = self.base_command + run_dump['run']['stdout'] = self.stdout + if self.stderr: + run_dump['run']['stderr'] = self.stderr + run_dump['run'].update(self.inputs.dump()) + run_dump['run'].update(self.outputs.dump()) + return run_dump + + def generate_in(self): + """Generate the in section for a task as well as the YAML for a particular step. + + This maps to the inputs part of the run section which is then + called in the step which holds that run section. + """ + in_ = {'in': {}} + for i in self.inputs.inputs: + if i.source: + in_['in'][i.input_name] = i.source + else: + in_['in'][i.input_name] = i.input_name + return in_ + + def generate_out(self): + """Generate the out section for a task. + + This is the same as the in section, but it does require that + the outputs are a list to produce the proper CWL. + """ + out_keys = list(self.outputs.dump()['outputs'].keys()) + out_ = {'out': out_keys} + return out_ + + def __repr__(self): + """Return Run as a yaml string.""" + return yaml.dump(self.dump(), sort_keys=False) + + +class Step: + """Represent a CWL step.""" + + def __init__(self, step_name, run, hints=None): + """Initialize CWL step.""" + self.step_name = step_name + self.run = run + self.in_ = run.generate_in() + self.out_ = run.generate_out() + self.hints = hints + + def dump(self): + """Dump step to a dictionary.""" + step_dump = {self.step_name: {}} + step_dump[self.step_name].update(self.run.dump()) + step_dump[self.step_name].update(self.in_) + step_dump[self.step_name].update(self.out_) + if self.hints: + step_dump[self.step_name].update(self.hints.dump()) + return step_dump + + def __repr__(self): + """Return CWL step as a string.""" + return yaml.dump(self.dump(), default_flow_style=None, sort_keys=False) + + +class Steps: + """Represent CWL steps.""" + + def __init__(self, steps): + """Initialize the CWL step.""" + self.steps = steps + + def dump(self): + """Dump steps to a dictionary.""" + steps_dump = {'steps': {}} + for step in self.steps: + steps_dump['steps'].update(step.dump()) + return steps_dump + + def __repr__(self): + """Dump the CWL steps.""" + return yaml.dump(self.dump(), default_flow_style=None, sort_keys=False) + + +class CWL: + """Class represents a CWL workflow and all its components.""" + + def __init__(self, cwl_name, inputs, outputs, steps): + """Initialize the CWL.""" + self.cwl_name = cwl_name + self.header = Header() + self.inputs = inputs + self.outputs = outputs + self.steps = steps + + def dump_wf(self, path=None): + """Dump the workflow. If no path is specified print to stdout.""" + cwl_dump = {} + cwl_dump.update(self.header.dump()) + cwl_dump.update(self.inputs.dump()) + cwl_dump.update(self.outputs.dump()) + cwl_dump.update(self.steps.dump()) + wf_contents = yaml.dump(cwl_dump, sort_keys=False) + if path: + with open(f"{path}/{self.cwl_name}.cwl", "w", encoding="utf-8") as wf_file: + print(wf_contents, file=wf_file) + return wf_contents + + def dump_inputs(self, path=None): + """Dump YAML inputs.""" + yaml_contents = yaml.dump(self.inputs.generate_yaml_inputs(), + sort_keys=False) + if path: + with open(f"{path}/{self.cwl_name}.yml", "w", encoding="utf-8") as yaml_file: + print(yaml_contents, file=yaml_file) + return yaml_contents + + def __repr__(self): + """Return CWL file as a string.""" + return yaml.dump(self.dump_wf(), sort_keys=False) diff --git a/beeflow/common/cwl/examples/cat_grep_tar_driver.py b/beeflow/common/cwl/examples/cat_grep_tar_driver.py new file mode 100644 index 000000000..287722316 --- /dev/null +++ b/beeflow/common/cwl/examples/cat_grep_tar_driver.py @@ -0,0 +1,75 @@ +"""Cat grep tar driver for CWL generator.""" +import pathlib +from beeflow.common.cwl.cwl import (CWL, CWLInput, RunInput, Inputs, CWLOutput, + CWLInputs, Outputs, Run, RunOutput, Step, Steps, + InputBinding) + + +def main(): + """Recreate the COMD workflow.""" + # CWLInputs + cwl_inputs = CWLInputs([CWLInput("input_file", "File", value="lorem.txt"), + CWLInput("word0", "string", value="Vivamus"), + CWLInput("word1", "string", value="pulvinar"), + CWLInput("tarball_fname", "string", value="out.tgz") + ]) + + # CWLOutputs + cwl_outputs = Outputs([CWLOutput("tarball", "File", "tar/tarball"), + CWLOutput("cat_stderr", "File", "cat/cat_stderr")]) + + # Step Cat + base_command = "cat" + stdout = "cat.txt" + stderr = "cat.err" + cat_inputs = Inputs([RunInput("input_file", "File", InputBinding(position=1))]) + cat_outputs = Outputs([RunOutput("contents", "stdout"), RunOutput("cat_stderr", "stderr")]) + cat_run = Run(base_command, cat_inputs, cat_outputs, stdout, stderr) + cat_step = Step("cat", cat_run) + + # Step Grep0 + base_command = "grep" + stdout = "occur0.txt" + run_inputs = Inputs([RunInput("word", "string", + InputBinding(position=1), source="word0"), + RunInput("text_file", "File", + InputBinding(position=2), source="cat/contents")]) + run_outputs = Outputs([RunOutput("occur", "stdout")]) + grep0_run = Run(base_command, run_inputs, run_outputs, stdout, stderr) + grep0_step = Step("grep0", grep0_run) + + # Step Grep1 + base_command = "grep" + stdout = "occur1.txt" + run_inputs = Inputs([RunInput("word", "string", + InputBinding(position=1), source="word1"), + RunInput("text_file", "File", + InputBinding(position=2), source="cat/contents")]) + run_outputs = Outputs([RunOutput("occur", "stdout")]) + grep1_run = Run(base_command, run_inputs, run_outputs, stdout, stderr) + grep1_step = Step("grep1", grep1_run) + + # Step Tar + base_command = "tar" + stdout = "tar.txt" + run_inputs = Inputs([RunInput("tarball_fname", "string", + InputBinding(position=1, prefix="-cf")), + RunInput("file0", "File", + InputBinding(position=2), source="grep0/occur"), + RunInput("file1", "File", + InputBinding(position=3), source="grep1/occur")]) + run_outputs = Outputs([RunOutput("tarball", "File")]) + tar_run = Run(base_command, run_inputs, run_outputs, stdout, stderr) + tar_step = Step("tar", tar_run) + + cgt_steps = Steps([cat_step, grep0_step, grep1_step, tar_step]) + cgt = CWL("catgreptar", cwl_inputs, cwl_outputs, cgt_steps) + + cgt_path = pathlib.Path("cat-grep-tar/") + cgt_path.mkdir(exist_ok=True) + cgt.dump_wf(cgt_path) + cgt.dump_inputs(cgt_path) + + +if __name__ == "__main__": + main() diff --git a/beeflow/common/cwl/examples/comd_driver.py b/beeflow/common/cwl/examples/comd_driver.py new file mode 100644 index 000000000..cdf4f821a --- /dev/null +++ b/beeflow/common/cwl/examples/comd_driver.py @@ -0,0 +1,50 @@ +"""COMD driver for CWL generator.""" +import pathlib +from beeflow.common.cwl.cwl import (CWL, CWLInput, CWLInputs, RunInput, Inputs, CWLOutput, + Outputs, Run, RunOutput, Step, Steps, + InputBinding, MPIRequirement, DockerRequirement, Hints) + + +def main(): + """Recreate the COMD workflow.""" + # CWLInputs + cwl_inputs = CWLInputs([CWLInput('i', 'int', value=2), + CWLInput('j', 'int', value=2), + CWLInput('k', 'int', value=2), + CWLInput('x', 'int', value=40), + CWLInput('y', 'int', value=40), + CWLInput('z', 'int', value=40), + CWLInput('pot_dir', 'string', value='/CoMD/pots')]) + + # CWLOutputs + cwl_outputs = Outputs([CWLOutput('comd_stdout', 'File', 'comd/comd_stdout')]) + + # Step Run + base_command = "'[/CoMD/bin/CoMD-mpi, '-e']'" + stdout = 'comd_stdout.txt' + run_inputs = Inputs([RunInput('i', 'int', InputBinding(prefix='-i')), + RunInput('j', 'int', InputBinding(prefix='-j')), + RunInput('k', 'int', InputBinding(prefix='-k')), + RunInput('x', 'int', InputBinding(prefix='-x')), + RunInput('y', 'int', InputBinding(prefix='-y')), + RunInput('z', 'int', InputBinding(prefix='-z')), + RunInput('pot_dir', 'string', InputBinding(prefix='--potDir'))]) + + run_outputs = Outputs([RunOutput('comd_stdout', 'stdout')]) + mpi = MPIRequirement(nodes=4, ntasks=8) + container_path = '/usr/projects/beedev/mpi/comd-x86_64.tgz' + docker = DockerRequirement(copy_container=container_path) + hints = Hints(mpi_requirement=mpi, docker_requirement=docker) + comd_run = Run(base_command, run_inputs, run_outputs, stdout) + comd_step = Step('comd', comd_run, hints) + comd_steps = Steps([comd_step]) + comd = CWL('comd', cwl_inputs, cwl_outputs, comd_steps) + + comd_path = pathlib.Path("comd/") + comd_path.mkdir(exist_ok=True) + comd.dump_wf(comd_path) + comd.dump_inputs(comd_path) + + +if __name__ == "__main__": + main() diff --git a/beeflow/common/db/tm_db.py b/beeflow/common/db/tm_db.py index 42383b22a..8e9666dc1 100644 --- a/beeflow/common/db/tm_db.py +++ b/beeflow/common/db/tm_db.py @@ -5,6 +5,7 @@ from beeflow.common.db import bdb from beeflow.common import log as bee_logging +from beeflow.common.wf_data import TaskStateUpdate log = bee_logging.setup(__name__) @@ -116,6 +117,41 @@ def clear(self): bdb.run(self.db_file, stmt) +class UpdateQueue: + """Task Manager update queue.""" + + def __init__(self, db_file): + """Construct an update queue handler.""" + self.db_file = db_file + + def push(self, wf_id, task_id, job_state, task_info=None, metadata=None, output=None): + """Push an update onto the update queue.""" + stmt = """INSERT INTO update_queue (wf_id, task_id, job_state, task_info, metadata, output) + VALUES (:wf_id, :task_id, :job_state, :task_info, :metadata, :output)""" + bdb.run(self.db_file, stmt, {'wf_id': wf_id, 'task_id': task_id, + 'job_state': job_state, + 'task_info': jsonpickle.encode(task_info), + 'metadata': jsonpickle.encode(metadata), + 'output': jsonpickle.encode(output)}) + + def updates(self): + """Get a list of all updates from the update queue.""" + stmt = """SELECT wf_id, task_id, job_state, task_info, metadata, output + FROM update_queue ORDER BY id ASC""" + state_updates = [] + for result in bdb.getall(self.db_file, stmt): + wf_id, task_id, job_state, task_info, metadata, output = result + state_updates.append(TaskStateUpdate(wf_id, task_id, job_state, + jsonpickle.decode(task_info), + jsonpickle.decode(metadata), + jsonpickle.decode(output))) + return state_updates + + def clear(self): + """Clear the update queue.""" + bdb.run(self.db_file, 'DELETE FROM update_queue') + + class TMDB: """Task Manager Database.""" @@ -136,8 +172,18 @@ def _init_tables(self): job_id INTEGER, job_state TEXT)""" + update_queue_stmt = """CREATE TABLE IF NOT EXISTS update_queue( + id INTEGER PRIMARY KEY ASC, + wf_id TEXT, + task_id TEXT, + job_state TEXT, + task_info TEXT, + metadata TEXT, + output TEXT)""" + bdb.create_table(self.db_file, submit_queue_stmt) bdb.create_table(self.db_file, job_queue_stmt) + bdb.create_table(self.db_file, update_queue_stmt) @property def submit_queue(self): @@ -149,6 +195,11 @@ def job_queue(self): """Return a JobQueue object.""" return JobQueue(self.db_file) + @property + def update_queue(self): + """Return an UpdateQueue object.""" + return UpdateQueue(self.db_file) + def open_db(db_file): """Open and return a new database.""" diff --git a/beeflow/common/db/wfm_db.py b/beeflow/common/db/wfm_db.py index d1f7dd8d6..63cc87456 100644 --- a/beeflow/common/db/wfm_db.py +++ b/beeflow/common/db/wfm_db.py @@ -10,7 +10,7 @@ class WorkflowInfo: def __init__(self, db_file): """Initialize Info and db file.""" - self.Info = namedtuple("Info", "id wfm_port tm_port sched_port num_workflows") # noqa Snake Case + self.Info = namedtuple("Info", "id wfm_port tm_port sched_port num_workflows bolt_port http_port https_port gdb_pid") # noqa Snake Case self.db_file = db_file def set_port(self, component, new_port): @@ -22,7 +22,7 @@ def get_port(self, component): """Return port for the specified component.""" # Need to add code here to make sure we chose a valid component. stmt = f"SELECT {component}_port FROM info" - result = bdb.getone(self.db_file, stmt) + result = bdb.getone(self.db_file, stmt)[0] port = result return port @@ -45,6 +45,18 @@ def get_info(self): info = self.Info(*result) return info + def get_gdb_pid(self): + """Return the gdb pid.""" + stmt = "SELECT gdb_pid FROM info" + result = bdb.getone(self.db_file, stmt)[0] + gdb_pid = result + return gdb_pid + + def update_gdb_pid(self, gdb_pid): + """Update the gdb PID.""" + stmt = "UPDATE info SET gdb_pid=?" + bdb.run(self.db_file, stmt, [gdb_pid]) + class Workflows: """Workflow database object.""" @@ -53,7 +65,7 @@ def __init__(self, db_file): """Initialize Task, db_file, and Workflow object.""" self.Task = namedtuple("Task", "id task_id workflow_id name resource state slurm_id") #noqa self.db_file = db_file - self.Workflow = namedtuple("Workflow", "id workflow_id name state run_dir bolt_port http_port https_port gdb_pid") #noqa + self.Workflow = namedtuple("Workflow", "id workflow_id name state run_dir") #noqa def get_workflow(self, workflow_id): """Return a workflow object.""" @@ -69,13 +81,11 @@ def get_workflows(self): workflows = [self.Workflow(*workflow) for workflow in result] return workflows - def init_workflow(self, workflow_id, name, run_dir, bolt_port, http_port, https_port): + def init_workflow(self, workflow_id, name, run_dir): """Insert a new workflow into the database.""" - stmt = """INSERT INTO workflows (workflow_id, name, state, run_dir, - bolt_port, http_port, https_port, gdb_pid) - VALUES(?, ?, ?, ?, ?, ?, ?, ?);""" - bdb.run(self.db_file, stmt, [workflow_id, name, 'Initializing', run_dir, - bolt_port, http_port, https_port, -1]) + stmt = """INSERT INTO workflows (workflow_id, name, state, run_dir) + VALUES(?, ?, ?, ?);""" + bdb.run(self.db_file, stmt, [workflow_id, name, 'Initializing', run_dir]) def delete_workflow(self, workflow_id): """Delete a workflow from the database.""" @@ -107,7 +117,7 @@ def delete_task(self, task_id, workflow_id): def update_task_state(self, task_id, workflow_id, state): """Update the state of a task.""" - stmt = "UPDATE tasks SET state=? WHERE task_id=? AND workflow_id=? " + stmt = "UPDATE tasks SET state=? WHERE task_id=? AND workflow_id=?" bdb.run(self.db_file, stmt, [state, task_id, workflow_id]) def get_tasks(self, workflow_id): @@ -123,28 +133,9 @@ def get_task(self, task_id, workflow_id): result = bdb.getone(self.db_file, stmt, [task_id, workflow_id]) return result - def get_bolt_port(self, workflow_id): - """Return the bolt port associated with a workflow.""" - stmt = "SELECT bolt_port FROM workflows WHERE workflow_id=?" - result = bdb.getone(self.db_file, stmt, [workflow_id])[0] - bolt_port = result - return bolt_port - - def get_gdb_pid(self, workflow_id): - """Return the bolt port associated with a workflow.""" - stmt = "SELECT gdb_pid FROM workflows WHERE workflow_id=?" - result = bdb.getone(self.db_file, stmt, [workflow_id])[0] - gdb_pid = result - return gdb_pid - - def update_gdb_pid(self, workflow_id, gdb_pid): - """Update the gdb PID associated with a workflow.""" - stmt = "UPDATE workflows SET gdb_pid=? WHERE workflow_id=?" - bdb.run(self.db_file, stmt, [gdb_pid, workflow_id]) - def get_run_dir(self, workflow_id): - """Return the bolt port associated with a workflow.""" - stmt = "SELECT run_dir FROM workflows WHERE workflow_id=?" + """Return the run directory.""" + stmt = "SELECT run_dir FROM info WHERE workflow_id=?" result = bdb.getone(self.db_file, stmt, [workflow_id])[0] run_dir = result return run_dir @@ -166,20 +157,18 @@ def _init_tables(self): workflow_id INTEGER UNIQUE, name TEXT, state TEST NOT NULL, - run_dir STR, - bolt_port INTEGER, - http_port INTEGER, - https_port INTEGER, - gdb_pid INTEGER);""" + run_dir STR + );""" tasks_stmt = """CREATE TABLE IF NOT EXISTS tasks ( id INTEGER PRIMARY KEY, - task_id INTEGER UNIQUE, + task_id INTEGER, workflow_id INTEGER NOT NULL, name TEXT, resource TEXT, state TEXT, slurm_id INTEGER, + UNIQUE(task_id, workflow_id) ON CONFLICT ABORT, FOREIGN KEY (workflow_id) REFERENCES workflows (workflow_id) ON DELETE CASCADE @@ -190,7 +179,11 @@ def _init_tables(self): wfm_port INTEGER, tm_port INTEGER, sched_port INTEGER, - num_workflows INTEGER + num_workflows INTEGER, + bolt_port INTEGER, + http_port INTEGER, + https_port INTEGER, + gdb_pid INTEGER );""" bdb.create_table(self.db_file, workflows_stmt) @@ -198,9 +191,9 @@ def _init_tables(self): if not bdb.table_exists(self.db_file, 'info'): bdb.create_table(self.db_file, info_stmt) # insert a new workflow into the database - stmt = """INSERT INTO info (wfm_port, tm_port, sched_port, num_workflows) - VALUES(?, ?, ?, ?);""" - bdb.run(self.db_file, stmt, [-1, -1, -1, 0]) + stmt = """INSERT INTO info (wfm_port, tm_port, sched_port, num_workflows, + bolt_port, http_port, https_port, gdb_pid) VALUES(?, ?, ?, ?, ?, ?, ?, ?);""" + bdb.run(self.db_file, stmt, [-1, -1, -1, 0, -1, -1, -1, -1]) @property def workflows(self): diff --git a/beeflow/common/celery.py b/beeflow/common/deps/celery_manager.py similarity index 100% rename from beeflow/common/celery.py rename to beeflow/common/deps/celery_manager.py diff --git a/beeflow/common/deps/container_manager.py b/beeflow/common/deps/container_manager.py new file mode 100755 index 000000000..8d3857844 --- /dev/null +++ b/beeflow/common/deps/container_manager.py @@ -0,0 +1,88 @@ +#!/usr/bin/env python3 + +"""Functions for managing the BEE depency container and associated bind mounts.""" + +import os +import shutil +import subprocess + +from beeflow.common.config_driver import BeeConfig as bc +from beeflow.common import paths +from celery import shared_task #noqa pylama can't find celery + + +class NoContainerRuntime(Exception): + """An exception for no container runtime like charliecloud or singularity.""" + + +def check_container_runtime(): + """Check if the container runtime is currently installed.""" + # Needs to support singuarity as well + if shutil.which("ch-convert") is None or shutil.which("ch-run") is None: + print("ch-convert or ch-run not found. Charliecloud required" + " for neo4j container.") + raise NoContainerRuntime('') + + +def make_dep_dir(): + """Make a new bee dependency container directory.""" + bee_workdir = paths.workdir() + bee_dir = f'{bee_workdir}/deps' + bee_dir_exists = os.path.isdir(bee_dir) + if not bee_dir_exists: + os.makedirs(bee_dir) + + +def get_dep_dir(): + """Return the dependency directory path.""" + bee_workdir = paths.workdir() + bee_container_dir = f'{bee_workdir}/deps/' + return bee_container_dir + + +def get_container_dir(dep_name): + """Return the depency container path.""" + container_name = dep_name + '_container' + return get_dep_dir() + container_name + + +def check_container_dir(dep_name): + """Return true if the container directory exists.""" + container_dir = get_container_dir(dep_name) + container_dir_exists = os.path.isdir(container_dir) + return container_dir_exists + + +def create_image(dep_name): + """Create a new BEE dependency container if one does not exist. + + By default, the container is stored in /tmp//beeflow/deps. + """ + # Can throw an exception that needs to be handled by the caller + check_container_runtime() + + image = bc.get('DEFAULT', dep_name + '_image') + + # Check for BEE dependency container directory: + container_dir_exists = check_container_dir(dep_name) + if container_dir_exists: + print(f"Already have {dep_name} container") + return + + make_dep_dir() + container_dir = get_container_dir(dep_name) + + # Build new dependency container + try: + subprocess.run(["ch-convert", "-i", "tar", "-o", "dir", + str(image), str(container_dir)], check=True) + except subprocess.CalledProcessError as error: + print(f"ch-convert failed: {error}") + shutil.rmtree(container_dir) + print(f"{dep_name} container mount directory {container_dir} removed") + return + + # If neo4j, make the certificates directory + if dep_name == 'neo4j': + container_certs_path = os.path.join(container_dir, 'var/lib/neo4j/certificates') + os.makedirs(container_certs_path, exist_ok=True) diff --git a/beeflow/common/deps/neo4j_manager.py b/beeflow/common/deps/neo4j_manager.py new file mode 100644 index 000000000..298710cd5 --- /dev/null +++ b/beeflow/common/deps/neo4j_manager.py @@ -0,0 +1,190 @@ +"""Contains methods for managing neo4j instance.""" +import socket +import os +import shutil +import re +import subprocess +import time + +from beeflow.wf_manager.resources import wf_utils +from beeflow.common.db import wfm_db + +from beeflow.common import paths +from beeflow.common.deps import container_manager + +from beeflow.common.config_driver import BeeConfig as bc +from beeflow.common import log as bee_logging + +# Define directories within module scope +bee_workdir = paths.workdir() +mount_dir = os.path.join(bee_workdir, 'gdb_mount') +data_dir = mount_dir + '/data' +logs_dir = mount_dir + '/logs' +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') + + +def get_open_port(): + """Return an open ephemeral port.""" + s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) + s.bind(("", 0)) + s.listen(1) + port = s.getsockname()[1] + s.close() + return port + + +def setup_ports(): + """Return three open ports for bolt, http, https.""" + # Get ports for neo4j to run + bolt_port = get_open_port() + http_port = get_open_port() + https_port = get_open_port() + + db = wf_utils.connect_db(wfm_db, wf_utils.get_db_path()) + + db.info.set_port('bolt', bolt_port) + db.info.set_port('http', http_port) + db.info.set_port('https', https_port) + return bolt_port, http_port, https_port + + +def setup_mounts(): + """Set up mount directories for the graph database.""" + os.makedirs(data_dir, exist_ok=True) + os.makedirs(logs_dir, exist_ok=True) + 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): + """Set up GDB configuration. + + This function needs to be run before each new invocation since the + config file could have changed. + """ + os.makedirs(confs_dir, exist_ok=True) + gdb_configfile = shutil.copyfile(container_path + "/var/lib/neo4j/conf/neo4j.conf", + confs_dir + "/neo4j.conf") + log.info(gdb_configfile) + + with open(gdb_configfile, "rt", encoding="utf8") as cfile: + data = cfile.read() + + log.info(f"new bolt: {bolt_port}") + bolt_config = r'#(server.bolt.listen_address=):[0-9]*' + data = re.sub(bolt_config, rf'\1:{bolt_port}', data) + http_config = r'#(server.http.listen_address=):[0-9]*' + data = re.sub(http_config, rf'\1:{http_port}', data) + 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) + + 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.""" + db_password = bc.get('graphdb', 'dbpass') + try: + command = ['neo4j-admin', 'dbms', 'set-initial-password', str(db_password)] + 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: + log.error("neo4j-admin set-initial-password failed") + + +def create_database(): + """Create the neo4j database and return the process.""" + try: + command = ['neo4j', 'console'] + 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() + return proc + + except FileNotFoundError: + log.error("Neo4j failed to start.") + return -1 + + +def start(): + """Start the graph database.""" + log.info('Starting Neo4j Database') + + bolt_port, http_port, https_port = setup_ports() + + setup_configs(bolt_port, http_port, https_port) + + setup_mounts() + + create_credentials() + + return create_database() + + +def wait_gdb(): + """Need to wait for the GDB. Currently, we're using the sleep time paramater. + + We'd like to remove that in the future. + """ + gdb_sleep_time = bc.get('graphdb', 'sleep_time') + print(f'waiting {gdb_sleep_time}s for GDB to come up') + time.sleep(gdb_sleep_time) + + +def remove_gdb(): + """Remove the current GDB bind mount directory.""" + gdb_workdir = os.path.join(bee_workdir, 'current_gdb') + old_gdb_workdir = os.path.join(bee_workdir, 'old_gdb') + if os.path.isdir(gdb_workdir): + # Rename the directory to guard against NFS errors + shutil.move(gdb_workdir, old_gdb_workdir) + time.sleep(2) + shutil.rmtree(old_gdb_workdir) + time.sleep(2) diff --git a/beeflow/common/deps/redis_manager.py b/beeflow/common/deps/redis_manager.py new file mode 100644 index 000000000..68d8fd7d1 --- /dev/null +++ b/beeflow/common/deps/redis_manager.py @@ -0,0 +1,37 @@ +"""Module contains the code for launching redis subprocess.""" +import os +import subprocess + +from beeflow.common import paths + + +def start(log): + """Start redis.""" + data_dir = 'data' + os.makedirs(os.path.join(paths.redis_root(), data_dir), exist_ok=True) + conf_name = 'redis.conf' + container_path = paths.redis_container() + # Dump the config + conf_path = os.path.join(paths.redis_root(), conf_name) + if not os.path.exists(conf_path): + with open(conf_path, 'w', encoding='utf-8') as fp: + # Don't listen on TCP + print('port 0', file=fp) + print('dir', os.path.join('/mnt', data_dir), file=fp) + print('maxmemory 2mb', file=fp) + print('unixsocket', os.path.join('/mnt', paths.redis_sock_fname()), file=fp) + print('unixsocketperm 700', file=fp) + cmd = [ + 'ch-run', + f'--bind={paths.redis_root()}:/mnt', + container_path, + 'redis-server', + '/mnt/redis.conf', + ] + # Ran into a strange "Failed to configure LOCALE for invalid locale name." + # from Redis, so setting LANG=C. This could have consequences for UTF-8 + # strings. + env = dict(os.environ) + env['LANG'] = 'C' + env['LC_ALL'] = 'C' + return subprocess.Popen(cmd, env=env, stdout=log, stderr=log) diff --git a/beeflow/common/gdb/DESIGN.md b/beeflow/common/gdb/DESIGN.md index 64ea0b48c..c26763a24 100644 --- a/beeflow/common/gdb/DESIGN.md +++ b/beeflow/common/gdb/DESIGN.md @@ -1,83 +1,74 @@ -## DRAFT: Preliminary Design +# Graph Database Design -### Basics +## Basics A Neo4j graph consists of nodes and relationships. Nodes can have labels (e.g. `:Label`) and properties (name value pairs like `name = "Pat"`). Relationships have a type (e.g. `:DEPENDS_ON`) and properties. Property values can be `number`, `string`, `boolean`, spatial (only `Point`), temporal (e.g. `Time`, `Date`, `Duration`), or composite types of the previous types (e.g. lists and maps). -### BEE Workflow Graph Entities +## BEE Workflow Graph Entities -A BEE workflow is a DAG (currently implemented in Neo4j) that represents a workflow originally specified in a CWL (Common Workflow Language) file. The fundamental structure of the workflow is based on `Task` nodes and `DEPENDS_ON` relationships. There are other nodes and relationships that are used to represent other properties of the workflow such as `Metadata`, `Requirements`, `Hints`, `REQUIRES`, etc. BEE's nodes, relationships, and properties are documented below. +A BEE workflow is a DAG (currently implemented in Neo4j) that represents a workflow originally specified in a CWL (Common Workflow Language) file. The fundamental structure of the workflow is based on `Task` nodes and `DEPENDS_ON` relationships. There are other nodes and relationships that are used to represent other properties of the workflow such as `Metadata`, `Requirements`, `Hints`, `Inputs`, `Outputs`, etc. BEE's nodes, relationships, and properties are documented below. -### `:Task` +## List of Node Types +* Listed edges are **outgoing**. Nodes are english cased, edges are all caps. -* `task_id`: unique ID for every task in workflow -* `name`: name of task as a string -* `command`: command (and parameters) to be executed -* `inputs`: array of inputs to task -* `outputs`: array of outputs of task -* `state`: state of task during execution of workflow - - Still designing, but may be one of: - - `WAITING`: These tasks are in the database and are waiting for the tasks that they are dependent on to `COMPLETE` - - `READY`: These tasks are ready to be executed (sent to the task manager). The tasks they depend on are `COMPLETE` so al their inputs are available. - - `SUBMITTED`: These tasks have been sent to to the task manager but we don't know that they're actually `RUNNING` until we hear that from the task manager. - - `SUBMIT_FAIL`: The task manager attempted to submit a job for this task but there was a failure. - - `PENDING`: The task has been submitted and the ensuing job is pending execution on the machine, message via task manager. - - `RUNNING`: The task is actively executing on the machine. The task manager told us that this is true. - - `CANCELLED`: The task has stopped because it was told to by the user or other entity. The task is not `COMPLETE` and tasks that depend on it can not be run (we can't assume all of its outputs were successfully created). The task manager tells us that the task was `CANCELLED`. - - `CRASHED`: An abnormal termination. In other respects it's the same as `CANCELLED`. - - `ZOMBIE`: We may use this to indicate an unknown state after a system crash or loss of connection to the task manager or if during query loop the task manager gets an error when trying to query for it. Maybe. - - `COMPLETE`: The task has successfully completed execution and all of its outputs have been produced. Its dependent tasks may now be set to `READY`. -* `:DEPENDS_ON`: relationship(s) to `:Task`s that must complete before this task can run - - This relationship has no properties -* `:HAS_METADATA`: relationship to `:TaskMetadata` for this task - - This relationship has no properties -* `:HAS_REQUIREMENTS`: relationship to `:TaskRequirements` (must have) for this task - - This relationship has no properties -* `:HAS_HINTS`: relationship to `:TaskHints` (may have) for this task - - This relationship has no properties - -#### `:TaskMedatata`, `:Metadata` - -`:TaskMetadata` is also labelled as `:Metadata`. This is so that we can easily search the database for all metadata nodes (e.g. `:TaskMetadata`, `:WorkflowMetadata`). - -#### `:TaskRequirements`, `:Requirements` - -`:TaskRequirements` is also labelled as `:Requirements`. This is so that we can easily search the database for all requirements nodes (e.g. `:TaskRequirements`, `:WorkflowRequirements`). - -#### `:TaskHints`, `:Hints` - -`:TaskHints` is also labelled as `:Hints`. This is so that we can easily search the database for all hint nodes (e.g. `:TaskHints`, `:WorkflowHints`). +### `:BEE` +* This is the head node to the Graph Database. All `:Workflow` nodes point to this head. Only one such node exists in the graph database. +* `name`: Is always named "Head" ### `:Workflow` - -* `workflow_id`: unique ID for the **single** workflow in this database +* Node representing a workflow +* `id`: unique ID for a workflow in this database * `name`: name of workflow as a string -* `inputs`: array of inputs to workflow -* `outputs`: array of outputs of workflow * `state`: state of entire workflow - - Still designing, but may be one of: - - `WAITING`: The workflow has been loaded into the database and is waiting to be started. - - `RUNNING`: The actively is actively executing on the machine. - - `CANCELLED`: The task has stopped because it was told to by the user or other entity. Examine the tasks in the database to determine their individual status. - - `CRASHED`: An abnormal termination. In other respects it's the same as `CANCELLED`. - - `ZOMBIE`: We may use this to indicate an unknown state after a system crash or loss of connection to other parts of the system (client, task manager, etc.) - - `COMPLETE`: The workflow has successfully completed execution and all of its outputs have been produced. -* `:HAS_METADATA`: relationship to `:WorkflowMetadata` for this workflow - - This relationship has no properties -* `:HAS_REQUIREMENTS`: relationship to `:WorkflowRequirements` (must have) for this workflow - - This relationship has no properties -* `:HAS_HINTS`: relationship to `:WorkflowHints` (may have) for this workflow - - This relationship has no properties - -#### `:WorkflowMedatata`, `:Metadata` + - See `states,py` for more information +* `:WORKFLOW_OF`: Edge between from `:Workflow` to `:BEE` node to denote workflows of a BEE instance -`:WorkflowMetadata` is also labelled as `:Metadata`. This is so that we can easily search the database for all metadata nodes (e.g. `:TaskMetadata`, `:WorkflowMetadata`). - -#### `:WorkflowRequirements`, `:Requirements` - -`:WorkflowRequirements` is also labelled as `:Requirements`. This is so that we can easily search the database for all requirements nodes (e.g. `:TaskRequirements`, `:WorkflowRequirements`). +### `:Task` +* Node representing a single task in a workflow +* `id`: unique ID for every task in workflow +* `workflow_id`: `id` of the workflow the task belongs to +* `name`: name of task as a string +* `base_command`: command (and parameters) to be executed +* `stdout`: command output location for task +* `stdin`: error output location for task +* `:BEGINS`: Edge from `:Task` to `:Workflow` node to indicate using an input parameter from the workflow +* `:DEPENDS_ON`: Edge from a `:Task`(1) to a `:Task`(2). (2) must be completed before (1) can be submitted to the task manager. `:DEPENDS_ON` relationships are deduced by parsing CWL. + +### `:Input` +* Node that contains information for an input either to a workflow or task +* `id`: Moniker for input +* `type` Type of input (e.g File, string) +* `value` Value of input +* `:INPUT_OF`: Edge from `:Input` to either `:Task` or `:Workflow` node to indicate being an input to the workflow or task +#### IF `:Input` node is `:INPUT_OF` a `:Task` node: +* `position`: Serial number for multiple inputs +* `source`: + +### `:Output` +* Node that contains information for an output either from a workflow or task +* `id`: Moniker for output +* `type` Type of output (e.g File, string) +* `value` Value of output +* `:OUTPUT_OF`: Edge from `:Output` to either `:Task` or `:Workflow` node to indicate being an output of the task or workflow. +#### If `:Output` node is `:OUTPUT_OF` a `:Workflow` node: +* `source`: +#### IF `:Output` node is `:OUTPUT_OF` a `:Task` node: +* `glob`: + +### `:Hint` +* Node specifying hints (optional parameters) for a task or workflow +* `params`: Array of hint parameters for workflow or task +* `:HINT_OF`: Edge from `:Hint` to either `:Task` or `:Workflow` node to indicate being a hint of task or workflow + +### `:Requirement` +* Node specifying requirements (mandatory parameters) for a task or workflow +* `params`: Array of requirement parameters for workflow or task +* `:REQUIREMENT_OF`: Edge from `:Requirement` to either`:Task` or `:Workflow` node to indicate being a requirement of task or workflow + +### `Metadata` +* Contains state of task in workflow +* `state`: State of the task being described (defaults to `WAITING`) +* :DESCRIBES`: edge to the `:Task` node whose metadata is being described -#### `:WorkflowHints`, `:Hints` -`:WorkflowHints` is also labelled as `:Hints`. This is so that we can easily search the database for all hint nodes (e.g. `:TaskHints`, `:WorkflowHints`). diff --git a/beeflow/common/gdb/gdb_driver.py b/beeflow/common/gdb/gdb_driver.py index 16d225590..226b638d6 100644 --- a/beeflow/common/gdb/gdb_driver.py +++ b/beeflow/common/gdb/gdb_driver.py @@ -57,7 +57,7 @@ def reset_workflow(self, new_id): """ @abstractmethod - def load_task(self, task): + def load_task(self, task, task_state): """Load a task into a stored workflow. Dependencies should be automatically deduced and generated by the graph database @@ -284,17 +284,10 @@ def workflow_completed(self): :rtype: bool """ - @abstractmethod - def empty(self): - """Determine if the database is empty. - - :rtype: bool - """ - - @abstractmethod - def cleanup(self): - """Clean up all the data stored in the graph database.""" - @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 8a48d0059..597479c49 100644 --- a/beeflow/common/gdb/neo4j_cypher.py +++ b/beeflow/common/gdb/neo4j_cypher.py @@ -6,80 +6,93 @@ log = bee_logging.setup(__name__) +def create_bee_node(tx): + """Create a BEE node in the Neo4j database. + + This node connects to all workflows and allows them to exist in the same graph + """ + bee_query = ("MERGE (b:BEE {name:'Head'})") + + tx.run(bee_query) + + def create_workflow_node(tx, workflow): """Create a Workflow node in the Neo4j database. The workflow node is the entry point to the workflow. - :param workflow: the workflow description + + :param workflow: the workflow :type workflow: Workflow """ - workflow_query = ("CREATE (w:Workflow) " - "SET w.id = $workflow_id " + workflow_query = ("MATCH (b:BEE) " + "CREATE (b)<-[:WORKFLOW_OF]-(w:Workflow) " + "SET w.id = $wf_id " "SET w.name = $name " "SET w.state = $state") # Store the workflow ID and name in a new workflow node - tx.run(workflow_query, workflow_id=workflow.id, name=workflow.name, state=workflow.state) + tx.run(workflow_query, wf_id=workflow.id, name=workflow.name, state=workflow.state) -def create_workflow_hint_nodes(tx, hints): +def create_workflow_hint_nodes(tx, workflow): """Create Hint nodes for the workflow. - :param hints: the workflow hints - :type hints: list of Hint + :param workflow: the workflow whose hints to add to the graph + :type workflow: Workflow """ - for hint in hints: - hint_query = ("MATCH (w:Workflow) " + for hint in workflow.hints: + hint_query = ("MATCH (w:Workflow {id: $wf_id}) " "CREATE (w)<-[:HINT_OF]-(h:Hint $params) " "SET h.class = $class_") - tx.run(hint_query, params=hint.params, class_=hint.class_) + tx.run(hint_query, wf_id=workflow.id, params=hint.params, class_=hint.class_) -def create_workflow_requirement_nodes(tx, requirements): +def create_workflow_requirement_nodes(tx, workflow): """Create Requirement nodes for the workflow. - :param requirements: the workflow requirements - :type requirements: list of Requirement + :param workflow: the workflow whose requirements to add to the graph + :type workflow: Workflow """ - for req in requirements: - req_query = ("MATCH (w:Workflow) " + for req in workflow.requirements: + req_query = ("MATCH (w:Workflow {id: $wf_id}) " "CREATE (w)<-[:REQUIREMENT_OF]-(r:Requirement $params) " "SET r.class = $class_") - tx.run(req_query, params=req.params, class_=req.class_) + tx.run(req_query, wf_id=workflow.id, params=req.params, class_=req.class_) -def create_workflow_input_nodes(tx, inputs): +def create_workflow_input_nodes(tx, workflow): """Create Input nodes for the workflow. - :param inputs: the workflow inputs - :type inputs: list of InputParameter + :param workflow: the workflow whose inputs to add to the graph + :type workflow: Workflow """ - for input_ in inputs: - input_query = ("MATCH (w:Workflow) CREATE (w)<-[:INPUT_OF]-(i:Input) " + for input_ in workflow.inputs: + input_query = ("MATCH (w:Workflow {id: $wf_id}) CREATE (w)<-[:INPUT_OF]-(i:Input) " "SET i.id = $input_id " "SET i.type = $type " "SET i.value = $value") - tx.run(input_query, input_id=input_.id, type=input_.type, value=input_.value) + tx.run(input_query, wf_id=workflow.id, input_id=input_.id, type=input_.type, + value=input_.value) -def create_workflow_output_nodes(tx, outputs): +def create_workflow_output_nodes(tx, workflow): """Create Output nodes for the workflow. - :param outputs: the workflow outputs - :type outputs: list of OutputParameter + :param workflow: the workflow whose outputs to add to the graph + :type workflow: Workflow """ - for output in outputs: - output_query = ("MATCH (w:Workflow) CREATE (w)<-[:OUTPUT_OF]-(o:Output) " + for output in workflow.outputs: + output_query = ("MATCH (w:Workflow {id: $wf_id}) CREATE (w)<-[:OUTPUT_OF]-(o:Output) " "SET o.id = $output_id " "SET o.type = $type " "SET o.value = $value " "SET o.source = $source") - tx.run(output_query, output_id=output.id, type=output.type, value=output.value, - source=output.source) + tx.run(output_query, wf_id=workflow.id, output_id=output.id, type=output.type, + value=output.value, source=output.source) def create_task(tx, task): @@ -170,7 +183,7 @@ def create_task_output_nodes(tx, task): value=output.value, glob=output.glob) -def create_task_metadata_node(tx, task): +def create_task_metadata_node(tx, task, task_state): """Create a task metadata node in the Neo4j database. The node holds metadata about a task's execution state. @@ -179,9 +192,9 @@ def create_task_metadata_node(tx, task): :type task: Task """ metadata_query = ("MATCH (t:Task {id: $task_id}) " - "CREATE (m:Metadata {state: 'WAITING'})-[:DESCRIBES]->(t)") + "CREATE (m:Metadata {state: $task_state})-[:DESCRIBES]->(t)") - tx.run(metadata_query, task_id=task.id) + tx.run(metadata_query, task_id=task.id, task_state=task_state) def add_dependencies(tx, task, old_task=None, restarted_task=False): @@ -204,6 +217,7 @@ def add_dependencies(tx, task, old_task=None, restarted_task=False): "MATCH (t:Task)<-[:INPUT_OF]-(i:Input) " "WITH s, t, outputs, collect(i.source) as sources " "WHERE any(output IN outputs WHERE output IN sources) " + "AND (s.workflow_id = t.workflow_id) " "MERGE (t)-[:DEPENDS_ON]->(s)") tx.run(delete_dependencies_query, task_id=old_task.id) @@ -212,7 +226,7 @@ def add_dependencies(tx, task, old_task=None, restarted_task=False): else: begins_query = ("MATCH (s:Task {id: $task_id})<-[:INPUT_OF]-(i:Input) " "WITH s, collect(i.source) AS sources " - "MATCH (w:Workflow)<-[:INPUT_OF]-(i:Input) " + "MATCH (w:Workflow {id: s.workflow_id})<-[:INPUT_OF]-(i:Input) " "WITH s, w, sources, collect(i.id) AS inputs " "WHERE any(input IN sources WHERE input IN inputs) " "MERGE (s)-[:BEGINS]->(w)") @@ -221,15 +235,17 @@ def add_dependencies(tx, task, old_task=None, restarted_task=False): "MATCH (t:Task)<-[:OUTPUT_OF]-(o:Output) " "WITH s, t, sources, collect(o.id) as outputs " "WHERE any(input IN sources WHERE input IN outputs) " + "AND s.workflow_id = t.workflow_id " "MERGE (s)-[:DEPENDS_ON]->(t)") dependent_query = ("MATCH (s:Task {id: $task_id})<-[:OUTPUT_OF]-(o:Output) " "WITH s, collect(o.id) AS outputs " "MATCH (t:Task)<-[:INPUT_OF]-(i:Input) " "WITH s, t, outputs, collect(i.source) as sources " "WHERE any(output IN outputs WHERE output IN sources) " + "AND s.workflow_id = t.workflow_id " "MERGE (t)-[:DEPENDS_ON]->(s)") - tx.run(begins_query, task_id=task.id) + tx.run(begins_query, task_id=task.id, wf_id=task.workflow_id) tx.run(dependency_query, task_id=task.id) tx.run(dependent_query, task_id=task.id) @@ -239,11 +255,11 @@ 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): @@ -251,11 +267,11 @@ def get_task_hints(tx, task_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): @@ -263,11 +279,11 @@ def get_task_requirements(tx, task_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): @@ -275,11 +291,11 @@ def get_task_inputs(tx, task_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): @@ -287,102 +303,122 @@ def get_task_outputs(tx, task_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. +def get_workflow_by_id(tx, wf_id): + """Get the workflow from the Neo4j database. - :rtype: BoltStatementResult + :param wf_id: the workflow's ID + :type wf_id: str + :rtype: neo4j.Result """ - workflow_desc_query = "MATCH (w:Workflow) RETURN w" + workflow_query = "MATCH (w:Workflow {id: $wf_id}) RETURN w" - return tx.run(workflow_desc_query).single() + return tx.run(workflow_query, wf_id=wf_id).single()['w'] -def get_workflow_tasks(tx): +def get_workflow_tasks(tx, wf_id): """Get workflow tasks from the Neo4j database. - :rtype: BoltStatementResult + :param wf_id: the workflow's ID + :type wf_id: str + :rtype: neo4j.Result """ - workflow_query = "MATCH (t:Task) RETURN t" + workflow_query = "MATCH (t:Task) WHERE t.workflow_id = $wf_id RETURN t" - return tx.run(workflow_query) + return [rec['t'] for rec in tx.run(workflow_query, wf_id=wf_id)] -def get_workflow_requirements(tx): +def get_workflow_requirements(tx, wf_id): """Get workflow requirements from the Neo4j database. - :rtype: BoltStatementResult + :param wf_id: the workflow's ID + :type wf_id: str + :rtype: neo4j.Result """ - requirements_query = "MATCH (:Workflow)<-[:REQUIREMENT_OF]-(r:Requirement) RETURN r" + requirement_query = ("MATCH (:Workflow {id: $wf_id})<-[:REQUIREMENT_OF]-(r:Requirement) " + "RETURN r") - return tx.run(requirements_query) + return [rec['r'] for rec in tx.run(requirement_query, wf_id=wf_id)] -def get_workflow_hints(tx): +def get_workflow_hints(tx, wf_id): """Get workflow hints from the Neo4j database. - :rtype: BoltStatementResult + :param wf_id: the workflow's ID + :type wf_id: str + :rtype: neo4j.Result """ - hints_query = "MATCH (:Workflow)<-[:HINT_OF]-(h:Hint) RETURN h" + hints_query = "MATCH (:Workflow {id: $wf_id})<-[:HINT_OF]-(h:Hint) RETURN h" - return tx.run(hints_query) + return [rec['h'] for rec in tx.run(hints_query, wf_id=wf_id)] -def get_workflow_inputs(tx): +def get_workflow_inputs(tx, wf_id): """Get workflow inputs from the Neo4j database. - :rtype: BoltStatementResult + :param wf_id: the workflow's ID + :type wf_id: str + :rtype: neo4j.Result """ - inputs_query = "MATCH (:Workflow)<-[:INPUT_OF]-(i:Input) RETURN i" + inputs_query = "MATCH (:Workflow {id: $wf_id})<-[:INPUT_OF]-(i:Input) RETURN i" - return tx.run(inputs_query) + return [rec['i'] for rec in tx.run(inputs_query, wf_id=wf_id)] -def get_workflow_outputs(tx): +def get_workflow_outputs(tx, wf_id): """Get workflow outputs from the Neo4j database. - :rtype: BoltStatementResult + :param wf_id: the workflow's ID + :type wf_id: str + :rtype: neo4j.Result """ - outputs_query = "MATCH (:Workflow)<-[:OUTPUT_OF]-(o:Output) RETURN o" + outputs_query = "MATCH (:Workflow {id: $wf_id})<-[:OUTPUT_OF]-(o:Output) RETURN o" - return tx.run(outputs_query) + return [rec['o'] for rec in tx.run(outputs_query, wf_id=wf_id)] -def get_workflow_state(tx): +def get_workflow_state(tx, wf_id): """Get workflow state from the Neo4j database. + :param wf_id: the workflow's ID + :type wf_id: str :rtype: str """ - state_query = "MATCH (w:Workflow) RETURN w.state" + state_query = "MATCH (w:Workflow {id: $wf_id}) RETURN w.state" - return tx.run(state_query).single().value() + return tx.run(state_query, wf_id=wf_id).single().value() -def set_workflow_state(tx, state): +def set_workflow_state(tx, state, wf_id): """Get workflow state from the Neo4j database. :param state: the state the workflow will be set to :type state: str + :param wf_id: the workflow's ID + :type wf_id: str """ - state_query = "MATCH (w:Workflow) SET w.state = $state" + state_query = "MATCH (w:Workflow {id: $wf_id}) SET w.state = $state" - return tx.run(state_query, state=state) + return tx.run(state_query, state=state, wf_id=wf_id) -def get_ready_tasks(tx): +def get_ready_tasks(tx, wf_id): """Get all tasks that are ready to execute. - :rtype: BoltStatementResult + :param workflow_id: the workflow id + :type workflow_id: str + :rtype: neo4j.Result """ - get_ready_query = "MATCH (:Metadata {state: 'READY'})-[:DESCRIBES]->(t:Task) RETURN t" + get_ready_query = ("MATCH (:Metadata {state: 'READY'})-[:DESCRIBES]->" + "(t:Task {workflow_id: $wf_id}) RETURN t") - return tx.run(get_ready_query) + return [rec['t'] for rec in tx.run(get_ready_query, wf_id=wf_id)] def get_dependent_tasks(tx, task): @@ -390,11 +426,11 @@ def get_dependent_tasks(tx, 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 +464,11 @@ 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 +502,7 @@ 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 +532,7 @@ 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): @@ -547,30 +583,25 @@ def set_task_output_glob(tx, task, output_id, glob): tx.run(glob_query, task_id=task.id, output_id=output_id, glob=glob) -def set_init_tasks_to_ready(tx): - """Set the initial workflow tasks' states to 'READY'.""" - init_ready_query = ("MATCH (m:Metadata)-[:DESCRIBES]->(t:Task)-[:BEGINS]->(:Workflow) " - "WHERE NOT (t)-[:DEPENDS_ON]->(:Task) " - "SET m.state = 'READY'") - - tx.run(init_ready_query) +def set_init_task_inputs(tx, wf_id): + """Set the initial workflow tasks' inputs from workfow inputs or defaults if necessary. - -def set_init_task_inputs(tx): - """Set the initial workflow tasks' inputs from workfow inputs or defaults if necessary.""" - task_inputs_query = ("MATCH (i:Input)-[:INPUT_OF]->(:Task)-[:BEGINS]->(:Workflow)" + :param wf_id: the workflow id + :type wf_id: str + """ + task_inputs_query = ("MATCH (i:Input)-[:INPUT_OF]->(:Task)-[:BEGINS]->(:Workflow {id: $wf_id})" "<-[:INPUT_OF]-(wi:Input) " "WHERE i.source = wi.id AND wi.value IS NOT NULL " "SET i.value = wi.value") # Set any values to defaults if necessary - defaults_query = ("MATCH (i:Input)-[:INPUT_OF]->(t:Task)-[:BEGINS]->(:Workflow)" + defaults_query = ("MATCH (i:Input)-[:INPUT_OF]->(t:Task)-[:BEGINS]->(:Workflow {id: $wf_id})" "<-[:INPUT_OF]-(wi:Input) " "WHERE i.source = wi.id " "AND i.value IS NULL AND i.default IS NOT NULL " "SET i.value = i.default") - tx.run(task_inputs_query) - tx.run(defaults_query) + tx.run(task_inputs_query, wf_id=wf_id) + tx.run(defaults_query, wf_id=wf_id) def copy_task_outputs(tx, task): @@ -621,53 +652,61 @@ def set_paused_tasks_to_running(tx): tx.run(set_running_query) -def set_runnable_tasks_to_ready(tx): +def set_runnable_tasks_to_ready(tx, wf_id): """Set task states to 'READY' if all required inputs have values.""" set_runnable_ready_query = ("MATCH (m:Metadata)-[:DESCRIBES]->" - "(t:Task)<-[:INPUT_OF]-(i:Input) " + "(t:Task {workflow_id: $wf_id})<-[:INPUT_OF]-(i:Input) " "WITH m, t, collect(i) AS ilist " "WHERE m.state = 'WAITING' " "AND all(i IN ilist WHERE i.value IS NOT NULL) " "SET m.state = 'READY'") - tx.run(set_runnable_ready_query) + tx.run(set_runnable_ready_query, wf_id=wf_id) -def reset_tasks_metadata(tx): - """Reset the metadata for each of a workflow's tasks.""" - reset_metadata_query = ("MATCH (m:Metadata)-[:DESCRIBES]->(t:Task) " +def reset_tasks_metadata(tx, wf_id): + """Reset the metadata for each of a workflow's tasks. + + :param wf_id: the workflow's ID + :type wf_id: str + """ + reset_metadata_query = ("MATCH (m:Metadata)-[:DESCRIBES]->(t:Task {workflow_id: $wf_id}) " "DETACH DELETE m " "WITH t " "CREATE (:Metadata {state: 'WAITING'})-[:DESCRIBES]->(t)") - tx.run(reset_metadata_query) + tx.run(reset_metadata_query, wf_id=wf_id) -def reset_workflow_id(tx, new_id): +def reset_workflow_id(tx, old_id, new_id): """Reset the workflow ID of the workflow using uuid4. + :param old_id: the old workflow ID + :type old_id: str :param new_id: the new workflow ID :type new_id: str """ - reset_workflow_id_query = ("MATCH (w:Workflow), (t:Task) " + reset_workflow_id_query = ("MATCH (w:Workflow {id: $old_id}), (t:Task {workflow_id: $old_id}) " "SET w.id = $new_id " "SET t.workflow_id = $new_id") - tx.run(reset_workflow_id_query, new_id=new_id) + tx.run(reset_workflow_id_query, old_id=old_id, new_id=new_id) -def final_tasks_completed(tx): +def final_tasks_completed(tx, wf_id): """Return true if each of a workflow's final Task nodes has state 'COMPLETED'. + :param wf_id: the workflow's id + :type wf_id: str :rtype: bool """ - not_completed_query = ("MATCH (m:Metadata)-[:DESCRIBES]->(t:Task) " + not_completed_query = ("MATCH (m:Metadata)-[:DESCRIBES]->(t:Task {workflow_id: $wf_id}) " "WHERE NOT (t)<-[:DEPENDS_ON|:RESTARTED_FROM]-(:Task) " "AND m.state <> 'COMPLETED' " "RETURN t IS NOT NULL LIMIT 1") # False if at least one task with state not 'COMPLETED' - return bool(tx.run(not_completed_query).single() is None) + return bool(tx.run(not_completed_query, wf_id=wf_id).single() is None) def is_empty(tx): @@ -686,3 +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 3b3222576..99d273cf1 100644 --- a/beeflow/common/gdb/neo4j_driver.py +++ b/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 @@ -24,7 +24,7 @@ DEFAULT_PASSWORD = "password" -class Neo4JNotRunning(Exception): +class Neo4jNotRunning(Exception): """Exception thrown when connection attempted while Neo4j is not running.""" @@ -33,10 +33,17 @@ class Neo4jDriver(GraphDatabaseDriver): Implements GraphDatabaseDriver. Wraps the neo4j package proprietary driver. + This class is a SINGLETON and will always return the same instance of Neo4jDriver """ - def __init__(self, user=DEFAULT_USER, password=DEFAULT_PASSWORD, **kwargs): - """Create a new Neo4j database driver. + def __new__(cls): + """Create or get the instance of Neo4j database driver.""" + if not hasattr(cls, 'instance'): + cls.instance = super(Neo4jDriver, cls).__new__(cls) #noqa cls causing linting errors + return cls.instance + + def connect(self, user=DEFAULT_USER, password=DEFAULT_PASSWORD, **kwargs): + """Connect driver to the neo4j database. :param uri: the URI of the Neo4j database :type uri: str @@ -49,13 +56,19 @@ def __init__(self, user=DEFAULT_USER, password=DEFAULT_PASSWORD, **kwargs): bolt_port = kwargs.get("bolt_port", DEFAULT_BOLT_PORT) password = kwargs.get("db_pass", DEFAULT_PASSWORD) uri = f"bolt://{db_hostname}:{bolt_port}" - try: # Connect to the Neo4j database using the Neo4j proprietary driver - self._driver = Neo4jDatabase.driver(uri, auth=(user, password)) + self._driver = Neo4jDatabase.driver(uri, auth=(user, password)) #noqa outside init + # Checks the connection and returns ServiceUnavailable if something is wrong + self._driver.verify_connectivity() except ServiceUnavailable as sue: log.error("Neo4j database is unavailable") - raise Neo4JNotRunning("Neo4j database is unavailable") from sue + raise Neo4jNotRunning("Neo4j database is unavailable") from sue + + def create_bee_node(self): + """Create the "BEE" node for all workflows to connect to.""" + with self._driver.session() as session: + session.write_transaction(tx.create_bee_node) def initialize_workflow(self, workflow): """Begin construction of a workflow stored in Neo4j. @@ -67,35 +80,45 @@ def initialize_workflow(self, workflow): """ with self._driver.session() as session: session.write_transaction(tx.create_workflow_node, workflow) - session.write_transaction(tx.create_workflow_requirement_nodes, - requirements=workflow.requirements) - session.write_transaction(tx.create_workflow_hint_nodes, hints=workflow.hints) - session.write_transaction(tx.create_workflow_input_nodes, inputs=workflow.inputs) - session.write_transaction(tx.create_workflow_output_nodes, outputs=workflow.outputs) - - def execute_workflow(self): - """Begin execution of the workflow stored in the Neo4j database.""" - self._write_transaction(tx.set_init_task_inputs) - self._write_transaction(tx.set_init_tasks_to_ready) - self._write_transaction(tx.set_workflow_state, state='RUNNING') - - def pause_workflow(self): + session.write_transaction(tx.create_workflow_requirement_nodes, workflow) + session.write_transaction(tx.create_workflow_hint_nodes, workflow) + session.write_transaction(tx.create_workflow_input_nodes, workflow) + session.write_transaction(tx.create_workflow_output_nodes, workflow) + + def execute_workflow(self, workflow_id): + """Begin execution of a workflow stored in the Neo4j database. + + :param workflow_id: the workflow id + :type workflow_id: str + """ + self._write_transaction(tx.set_init_task_inputs, wf_id=workflow_id) + self._write_transaction(tx.set_runnable_tasks_to_ready, wf_id=workflow_id) + self._write_transaction(tx.set_workflow_state, state='RUNNING', wf_id=workflow_id) + + def pause_workflow(self, workflow_id): """Pause execution of a running workflow in Neo4j. Sets tasks with state 'RUNNING' to 'PAUSED'. + + :param workflow_id: the workflow id + :type workflow_id: str + """ with self._driver.session() as session: - session.write_transaction(tx.set_workflow_state, state='PAUSED') + session.write_transaction(tx.set_workflow_state, state='PAUSED', wf_id=workflow_id) - def resume_workflow(self): + def resume_workflow(self, workflow_id): """Resume execution of a paused workflow in Neo4j. - Sets workflow state to 'PAUSED' + Sets workflow state to 'RUNNING' + + :param workflow_id: the workflow id + :type workflow_id: str """ with self._driver.session() as session: - session.write_transaction(tx.set_workflow_state, state='RESUME') + session.write_transaction(tx.set_workflow_state, state='RUNNING', wf_id=workflow_id) - def reset_workflow(self, new_id): + def reset_workflow(self, old_id, new_id): """Reset the execution state of an entire workflow. Sets all task states to 'WAITING'. @@ -105,10 +128,10 @@ def reset_workflow(self, new_id): :type new_id: str """ with self._driver.session() as session: - session.write_transaction(tx.reset_tasks_metadata) - session.write_transaction(tx.reset_workflow_id, new_id=new_id) + session.write_transaction(tx.reset_tasks_metadata, wf_id=old_id) + session.write_transaction(tx.reset_workflow_id, old_id=old_id, new_id=new_id) - def load_task(self, task): + def load_task(self, task, task_state): """Load a task into a workflow stored in the Neo4j database. Dependencies are automatically deduced and generated by Neo4j upon loading @@ -125,15 +148,19 @@ def load_task(self, task): session.write_transaction(tx.create_task_requirement_nodes, task=task) session.write_transaction(tx.create_task_input_nodes, task=task) session.write_transaction(tx.create_task_output_nodes, task=task) - session.write_transaction(tx.create_task_metadata_node, task=task) + session.write_transaction(tx.create_task_metadata_node, task=task, + task_state=task_state) session.write_transaction(tx.add_dependencies, task=task) - def initialize_ready_tasks(self): + def initialize_ready_tasks(self, workflow_id): """Set runnable tasks to state 'READY'. Runnable tasks are tasks with all input dependencies fulfilled. + + :param workflow_id: the workflow id + :type workflow_id: str """ - self._write_transaction(tx.set_runnable_tasks_to_ready) + self._write_transaction(tx.set_runnable_tasks_to_ready, wf_id=workflow_id) def restart_task(self, old_task, new_task): """Restart a failed task. @@ -152,7 +179,8 @@ def restart_task(self, old_task, new_task): session.write_transaction(tx.create_task_requirement_nodes, task=new_task) session.write_transaction(tx.create_task_input_nodes, task=new_task) session.write_transaction(tx.create_task_output_nodes, task=new_task) - session.write_transaction(tx.create_task_metadata_node, task=new_task) + session.write_transaction(tx.create_task_metadata_node, task=new_task, + task_state="WAITING") session.write_transaction(tx.add_dependencies, task=new_task, old_task=old_task, restarted_task=True) @@ -177,73 +205,89 @@ def get_task_by_id(self, task_id): return _reconstruct_task(tuples[0][0], tuples[0][1], tuples[0][2], tuples[0][3], tuples[0][4]) - def get_workflow_description(self): + def get_workflow_description(self, workflow_id): """Return a reconstructed Workflow object from the Neo4j database. + :param workflow_id: the workflow id + :type workflow_id: str :rtype: Workflow """ - workflow_record = self._read_transaction(tx.get_workflow_description) - requirements, hints = self.get_workflow_requirements_and_hints() - inputs, outputs = self.get_workflow_inputs_and_outputs() + workflow_record = self._read_transaction(tx.get_workflow_by_id, wf_id=workflow_id) + requirements, hints = self.get_workflow_requirements_and_hints(workflow_id) + inputs, outputs = self.get_workflow_inputs_and_outputs(workflow_id) return _reconstruct_workflow(workflow_record, hints, requirements, inputs, outputs) - def get_workflow_state(self): + def get_workflow_state(self, workflow_id): """Return the current workflow state from the Neo4j database. + :param workflow_id: the workflow id + :type workflow_id: str :rtype: str """ - return self._read_transaction(tx.get_workflow_state) + return self._read_transaction(tx.get_workflow_state, wf_id=workflow_id) - def set_workflow_state(self, state): + def set_workflow_state(self, workflow_id, state): """Set the state of the workflow in the Neo4j database. + :param workflow_id: the workflow id + :type workflow_id: str :param state: the new state of the workflow :type state: str """ - self._write_transaction(tx.set_workflow_state, state=state) + self._write_transaction(tx.set_workflow_state, state=state, wf_id=workflow_id) - def get_workflow_tasks(self): - """Return all workflow task records from the Neo4j database. + def get_workflow_tasks(self, workflow_id): + """Return all workflow task records for a workflow from the Neo4j database. + :param workflow_id: the workflow id + :type workflow_id: str :rtype: list of Task """ - task_records = self._read_transaction(tx.get_workflow_tasks) + task_records = self._read_transaction(tx.get_workflow_tasks, wf_id=workflow_id) tuples = self._get_task_data_tuples(task_records) return [_reconstruct_task(tup[0], tup[1], tup[2], tup[3], tup[4]) for tup in tuples] - def get_workflow_requirements_and_hints(self): + def get_workflow_requirements_and_hints(self, workflow_id): """Return all workflow requirements and hints from the Neo4j database. Returns a tuple of (requirements, hints). + :param workflow_id: the workflow id + :type workflow_id: str :rtype: (list of Requirement, list of Hint) """ with self._driver.session() as session: requirements = _reconstruct_requirements( - session.read_transaction(tx.get_workflow_requirements)) - hints = _reconstruct_hints(session.read_transaction(tx.get_workflow_hints)) + session.read_transaction(tx.get_workflow_requirements, wf_id=workflow_id)) + hints = _reconstruct_hints(session.read_transaction(tx.get_workflow_hints, + wf_id=workflow_id)) return requirements, hints - def get_workflow_inputs_and_outputs(self): - """Return all workflow inputs and outputs from the Neo4j database. + def get_workflow_inputs_and_outputs(self, workflow_id): + """Return all workflow inputs and outputs for a workflow from the Neo4j database. Returns a tuple of (inputs, outputs). + :param workflow_id: the workflow id + :type workflow_id: str :rtype: (list of InputParameter, list of OutputParameter) """ with self._driver.session() as session: - inputs = _reconstruct_workflow_inputs(session.read_transaction(tx.get_workflow_inputs)) + inputs = _reconstruct_workflow_inputs(session.read_transaction(tx.get_workflow_inputs, + wf_id=workflow_id)) outputs = _reconstruct_workflow_outputs( - session.read_transaction(tx.get_workflow_outputs)) + session.read_transaction(tx.get_workflow_outputs, wf_id=workflow_id)) return inputs, outputs - def get_ready_tasks(self): - """Return tasks with state 'READY' from the graph database. + def get_ready_tasks(self, workflow_id): + """Return tasks with state 'READY' from the graph database from a particular workflow. + :param workflow_id: the workflow id + :type workflow_id: str :rtype: list of Task """ - task_records = self._read_transaction(tx.get_ready_tasks) + task_records = self._read_transaction(tx.get_ready_tasks, wf_id=workflow_id) tuples = self._get_task_data_tuples(task_records) return [_reconstruct_task(tup[0], tup[1], tup[2], tup[3], tup[4]) for tup in tuples] @@ -307,7 +351,7 @@ 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 +374,7 @@ 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. @@ -368,24 +412,15 @@ def set_task_output_glob(self, task, output_id, glob): """ self._write_transaction(tx.set_task_output_glob, task=task, output_id=output_id, glob=glob) - def workflow_completed(self): + def workflow_completed(self, workflow_id): """Determine if a workflow in the Neo4j database has completed. A workflow has completed if each of its final task nodes have state 'COMPLETED'. + :param workflow_id: the workflow id + :type workflow_id: str :rtype: bool """ - return self._read_transaction(tx.final_tasks_completed) - - def empty(self): - """Determine if the Neo4j database is empty. - - :rtype: bool - """ - return self._read_transaction(tx.is_empty) - - def cleanup(self): - """Clean up all data in the Neo4j database.""" - self._write_transaction(tx.cleanup) + return self._read_transaction(tx.final_tasks_completed, wf_id=workflow_id) def close(self): """Close the connection to the Neo4j database.""" @@ -401,13 +436,13 @@ 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] @@ -439,6 +474,11 @@ 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. @@ -447,9 +487,8 @@ 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 +498,8 @@ 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 +509,7 @@ 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 +519,8 @@ 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 +530,7 @@ 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 +551,7 @@ 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 +579,8 @@ 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 +598,10 @@ 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 +613,7 @@ 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 diff --git a/beeflow/common/gdb_interface.py b/beeflow/common/gdb_interface.py deleted file mode 100644 index ab49ea873..000000000 --- a/beeflow/common/gdb_interface.py +++ /dev/null @@ -1,302 +0,0 @@ -"""Mid-level interface for managing a graph database with workflows. - -Delegates the actual work to an instance of a subclass of -the abstract base class GraphDatabaseDriver. By default, -this is the Neo4jDriver class. -""" - -from beeflow.common.gdb.neo4j_driver import Neo4jDriver -from beeflow.common import expr - - -class GraphDatabaseInterface: - """Interface for managing a graph database with workflows. - - Requires an implemented subclass of GraphDatabaseDriver (uses Neo4jDriver by default). - """ - - def __init__(self, gdb_driver=Neo4jDriver): - """Initialize the graph database interface with a graph database driver. - - :param gdb_driver: the graph database driver (Neo4jDriver by default) - :type gdb_driver: subclass of GraphDatabaseDriver - """ - # Store the GDB driver state - self._connection = gdb_driver - - def __del__(self): - """Disconnect from the graph database when interface deconstructs.""" - if self.initialized(): - self.close() - - def connect(self, **kwargs): - """Initialize a graph database interface with a driver. - - :param kwargs: arguments for initializing the graph database connection - """ - - def initialize_workflow(self, workflow): - """Begin construction of a workflow in the graph database. - - Connects to the database and creates the Workflow with accompanying Hint - and Requirement nodes. - Permits the addition of task nodes to the workflow. - - :param workflow: the workflow description - :type workflow: Workflow - """ - self._connection.initialize_workflow(workflow) - - def execute_workflow(self): - """Begin execution of the loaded workflow.""" - self._connection.execute_workflow() - - def pause_workflow(self): - """Pause execution of a running workflow.""" - self._connection.pause_workflow() - - def resume_workflow(self): - """Resume execution of a running workflow.""" - self._connection.resume_workflow() - - def reset_workflow(self, new_id): - """Reset the execution state and ID of a workflow. - - :param new_id: the new workflow ID - :type new_id: str - """ - self._connection.reset_workflow(new_id) - - def load_task(self, task): - """Load a task into a workflow in the graph database. - - :param task: the task - :type task: Task - """ - self._connection.load_task(task) - - def initialize_ready_tasks(self): - """Set runnable tasks in a workflow to ready.""" - self._connection.initialize_ready_tasks() - - def restart_task(self, old_task, new_task): - """Create a new task from a failed task checkpoint restart enabled. - - :param old_task: the failed task - :type old_task: Task - :param new_task: the new (restarted) task - :type new_task: Task - """ - self._connection.restart_task(old_task, new_task) - - def finalize_task(self, task): - """Set a task's state to completed. - - :param task: the task to finalize - :type task: Task - """ - self._connection.finalize_task(task) - - def get_task_by_id(self, task_id): - """Return a workflow Task given its ID. - - :param task_id: the task's ID - :type task_id: str - :rtype: Task - """ - return self._connection.get_task_by_id(task_id) - - def get_workflow_description(self): - """Return the workflow description from the graph database. - - :rtype: Workflow - """ - return self._connection.get_workflow_description() - - def get_workflow_state(self): - """Return workflow's current state. - - :rtype: str - """ - return self._connection.get_workflow_state() - - def set_workflow_state(self, state): - """Return workflow's current state. - - :param state: the new state of the workflow - :type state: str - """ - self._connection.set_workflow_state(state) - - def get_workflow_tasks(self): - """Return a workflow's tasks from the graph database. - - :rtype: list of Task - """ - return self._connection.get_workflow_tasks() - - def get_workflow_requirements_and_hints(self): - """Return a tuple containing a list of requirements and a list of hints. - - The returned tuple format is (requirements, hints). - - :rtype: (list of Requirement, list of Hint) - """ - return self._connection.get_workflow_requirements_and_hints() - - def get_ready_tasks(self): - """Return the tasks in a workflow with state 'READY'. - - :rtype: list of Task - """ - return self._connection.get_ready_tasks() - - def get_dependent_tasks(self, task): - """Return the dependents of a task in a workflow. - - :param task: the task whose dependents to retrieve - :type task: Task - :rtype: list of Task - """ - return self._connection.get_dependent_tasks(task) - - def get_task_state(self, task): - """Return the state of a task. - - :param task: the task whose state to retrieve - :type task: Task - :rtype: str - """ - return self._connection.get_task_state(task) - - def set_task_state(self, task, state): - """Set the state of a task. - - :param task: the task whose state to set - :type task: Task - :param state: the new state - :type state: str - """ - return self._connection.set_task_state(task, state) - - def get_task_metadata(self, task): - """Return the job description metadata of a task. - - :param task: the task whose metadata to retrieve - :type task: Task - :rtype: dict - """ - return self._connection.get_task_metadata(task) - - def set_task_metadata(self, task, metadata): - """Set the job description metadata of a task. - - :param task: the task whose metadata to set - :type task: Task - :param metadata: the job description metadata - :type metadata: dict - """ - self._connection.set_task_metadata(task, metadata) - - def get_task_input(self, task, input_id): - """Get a task input object. - - :param task: the task whose input to retrieve - :type task: Task - :param input_id: the ID of the input - :type input_id: str - :rtype: StepInput - """ - return self._connection.get_task_input(task, input_id) - - def set_task_input(self, task, input_id, value): - """Set the value of a task input. - - :param task: the task whose input to set - :type task: Task - :param input_id: the ID of the input - :type input_id: str - :param value: str or int or float - """ - self._connection.set_task_input(task, input_id, value) - - def get_task_output(self, task, output_id): - """Get a task output object. - - :param task: the task whose output to retrieve - :type task: Task - :param output_id: the ID of the output - :type output_id: str - :rtype: StepOutput - """ - return self._connection.get_task_output(task, output_id) - - def set_task_output(self, task, output_id, value): - """Set the value of a task output. - - :param task: the task whose output to set - :type task: Task - :param output_id: the ID of the output - :type output_id: str - :param value: the output value to set - :type value: str or int or float - """ - self._connection.set_task_output(task, output_id, value) - - def evaluate_expression(self, task, id_, output): - """Evaluate a task input/output expression. - - Expression can be a parameter substitution or a string concatenation in a StepInput - valueFrom field or a StepOutput glob field. The only special variable supported - is self.path. - - :param task: the task whose expression to evaluate - :type task: Task - :param id_: the id of the step input/output - :type id_: str - :param output: true if output glob expression being evaluated, else false - :type output: bool - """ - # Get ground-truth task from database before doing anything - task = self._connection.get_task_by_id(task.id) - input_pairs = {input.id: input.value for input in task.inputs} - if output: - step_output = self._connection.get_task_output(task, id_) - val = expr.eval_output(input_pairs, step_output.glob) - if val is not None: - self._connection.set_task_output_glob(task, id_, val) - else: - step_input = self._connection.get_task_input(task, id_) - val = expr.eval_input(input_pairs, step_input.value_from) - self._connection.set_task_input_type(task, id_, "string") - self._connection.set_task_input(task, id_, val) - - def workflow_completed(self): - """Return true if all of a workflow's final tasks have completed, else false. - - :rtype: bool - """ - return self._connection.workflow_completed() - - def initialized(self): - """Return true if the database connection has been initialized, else false. - - :rtype: bool - """ - return bool(self._connection is not None) - - def empty(self): - """Return true if the graph database is empty, else false. - - :rtype: bool - """ - return self._connection.empty() - - def cleanup(self): - """Clean up all data in the graph database.""" - self._connection.cleanup() - - def close(self): - """Close the connection to the graph database.""" - self._connection.close() - self._connection = None diff --git a/beeflow/common/integration/utils.py b/beeflow/common/integration/utils.py index 981e0b97a..a3fc45ec2 100644 --- a/beeflow/common/integration/utils.py +++ b/beeflow/common/integration/utils.py @@ -58,7 +58,7 @@ def __init__(self, name, path, main_cwl, job_file, workdir, containers): self.path = path self.main_cwl = main_cwl self.job_file = job_file - self.workdir = workdir + self.workdir = Path(workdir) self.containers = containers self.wf_id = None self.tarball = None @@ -96,6 +96,11 @@ def task_states(self): """Get the task states of the workflow.""" return bee_client.query(self.wf_id)[1] + def get_task_state_by_name(self, name): + """Get the state of a task by name.""" + task_states = self.task_states + return [task_state for _, task_name, task_state in task_states if task_name == name][0] + def cleanup(self): """Clean up any leftover workflow data.""" # Remove the generated tarball @@ -243,5 +248,12 @@ def check_completed(workflow): def check_workflow_failed(workflow): """Ensure that the workflow completed in a Failed state.""" - ci_assert(workflow.status == 'Failed', + ci_assert(workflow.status == 'Archived/Failed', f'workflow did not fail as expected (final status: {workflow.status})') + + +def make_workflow_workdir(outer_workdir): + """Create a workdir for the workflow run output files.""" + workdir = os.path.join(outer_workdir, uuid.uuid4().hex) + os.makedirs(workdir) + return workdir diff --git a/beeflow/common/integration_test.py b/beeflow/common/integration_test.py index 1dbc5b65b..71fac9126 100644 --- a/beeflow/common/integration_test.py +++ b/beeflow/common/integration_test.py @@ -1,4 +1,5 @@ """BEE integration tests.""" +import glob from pathlib import Path import os import shutil @@ -20,8 +21,7 @@ def copy_container(outer_workdir): # `beeflow:copyContainer` workflow container_path = f'/tmp/copy_container-{uuid.uuid4().hex}.tar.gz' container_name = 'copy-container' - workdir = os.path.join(outer_workdir, uuid.uuid4().hex) - os.makedirs(workdir) + workdir = utils.make_workflow_workdir(outer_workdir) container = utils.Container(container_name, generated_workflows.DOCKER_FILE_PATH, container_path) workflow_path = os.path.join(outer_workdir, f'bee-cc-workflow-{uuid.uuid4().hex}') @@ -94,8 +94,7 @@ def docker_file(outer_workdir): workflow_path = os.path.join(outer_workdir, f'bee-df-workflow-{uuid.uuid4().hex}') # Copy the Dockerfile to the workdir path os.makedirs(workflow_path) - workdir = os.path.join(outer_workdir, uuid.uuid4().hex) - os.makedirs(workdir) + workdir = utils.make_workflow_workdir(outer_workdir) shutil.copy(generated_workflows.DOCKER_FILE_PATH, os.path.join(workflow_path, 'Dockerfile')) container_name = 'docker_file_test' docker_requirement = { @@ -132,8 +131,7 @@ def docker_pull(outer_workdir): """Prepare, then check that the `dockerPull` option was successful.""" # `dockerPull` workflow workflow_path = os.path.join(outer_workdir, f'bee-dp-workflow-{uuid.uuid4().hex}') - workdir = os.path.join(outer_workdir, uuid.uuid4().hex) - os.makedirs(workdir) + workdir = utils.make_workflow_workdir(outer_workdir) container_name = generated_workflows.BASE_CONTAINER docker_requirement = { 'dockerPull': container_name, @@ -171,8 +169,7 @@ def multiple_workflows(outer_workdir): workflow_data = [] workflows = [] for i in range(3): - workdir = os.path.join(outer_workdir, uuid.uuid4().hex) - os.makedirs(workdir) + workdir = utils.make_workflow_workdir(outer_workdir) workflow_path = Path(outer_workdir, uuid.uuid4().hex) main_cwl, job_file = generated_workflows.simple_workflow(workflow_path, output_file) workflow = utils.Workflow(f'multi-workflow-{i}', workflow_path, @@ -197,8 +194,7 @@ def multiple_workflows(outer_workdir): @TEST_RUNNER.add() def build_failure(outer_workdir): """Test running a workflow with a bad container.""" - workdir = os.path.join(outer_workdir, uuid.uuid4().hex) - os.makedirs(workdir) + workdir = utils.make_workflow_workdir(outer_workdir) workflow = utils.Workflow('build-failure', 'ci/test_workflows/build-failure', main_cwl='workflow.cwl', job_file='input.yml', workdir=workdir, containers=[]) @@ -210,11 +206,44 @@ def build_failure(outer_workdir): f'task was not in state BUILD_FAIL as expected: {task_state}') +@TEST_RUNNER.add() +def dependent_tasks_fail(outer_workdir): + """Test that dependent tasks don't run after a failure.""" + workdir = utils.make_workflow_workdir(outer_workdir) + workflow = utils.Workflow('failure-dependent-tasks', + 'ci/test_workflows/failure-dependent-tasks', + main_cwl='workflow.cwl', job_file='input.yml', + workdir=workdir, containers=[]) + yield [workflow] + utils.check_workflow_failed(workflow) + # Check each task state + fail_state = workflow.get_task_state_by_name('fail') + utils.ci_assert(fail_state == 'FAILED', + f'task fail did not fail as expected: {fail_state}') + for task in ['dependent0', 'dependent1', 'dependent2']: + task_state = workflow.get_task_state_by_name(task) + utils.ci_assert(task_state == 'DEP_FAIL', + f'task {task} did not get state DEP_FAIL as expected: {task_state}') + + +@TEST_RUNNER.add() +def pre_post_script(outer_workdir): + """Test that the beeflow:ScriptRequirement works.""" + workdir = utils.make_workflow_workdir(outer_workdir) + workflow = utils.Workflow('pre-post-script', 'ci/test_workflows/pre-post-script', + main_cwl='workflow.cwl', job_file='input.yml', + workdir=workdir, containers=[]) + yield [workflow] + utils.check_completed(workflow) + # Ensure files were touched by the pre and post scripts + utils.check_path_exists(Path(workdir, 'pre.txt')) + utils.check_path_exists(Path(workdir, 'post.txt')) + + @TEST_RUNNER.add(ignore=True) def checkpoint_restart(outer_workdir): """Test the clamr-ffmpeg checkpoint restart workflow.""" - workdir = os.path.join(outer_workdir, uuid.uuid4().hex) - os.makedirs(workdir) + workdir = utils.make_workflow_workdir(outer_workdir) workflow = utils.Workflow('checkpoint-restart', 'ci/test_workflows/clamr-wf-checkpoint', main_cwl='clamr_wf.cwl', job_file='clamr_job.yml', @@ -229,8 +258,7 @@ def checkpoint_restart(outer_workdir): @TEST_RUNNER.add(ignore=True) def checkpoint_restart_failure(outer_workdir): """Test a checkpoint restart workflow that continues past 'num_retries'.""" - workdir = os.path.join(outer_workdir, uuid.uuid4().hex) - os.makedirs(workdir) + workdir = utils.make_workflow_workdir(outer_workdir) workflow = utils.Workflow('checkpoint-too-long', 'ci/test_workflows/checkpoint-too-long', main_cwl='workflow.cwl', job_file='input.yml', @@ -239,6 +267,19 @@ def checkpoint_restart_failure(outer_workdir): utils.check_workflow_failed(workflow) +@TEST_RUNNER.add(ignore=True) +def comd_mpi(outer_workdir): + """Test the comd-mpi workflow.""" + workdir = utils.make_workflow_workdir(outer_workdir) + workflow = utils.Workflow('comd-mpi', 'ci/test_workflows/comd-mpi', + main_cwl='comd_wf.cwl', job_file='comd_job.yml', + workdir=workdir, containers=[]) + yield [workflow] + utils.check_completed(workflow) + fnames = glob.glob('CoMD-mpi.*.yaml', root_dir=workdir) + utils.ci_assert(len(fnames) > 0, 'missing comd output yaml file') + + def test_input_callback(arg): """Parse a list of tests separated by commas.""" return arg.split(',') if arg is not None else None diff --git a/beeflow/common/parser/parser.py b/beeflow/common/parser/parser.py index 7a03cddd1..840a7d3d2 100644 --- a/beeflow/common/parser/parser.py +++ b/beeflow/common/parser/parser.py @@ -97,12 +97,13 @@ def resolve_input(input_, type_): """ # Use parsed input parameter for input value if it exists input_id = _shortname(input_.id) - if input_id not in self.params: - return None - if not isinstance(self.params[input_id], type_map[type_]): + value = self.params[input_id] if input_id in self.params else input_.default + if value is None: + raise CwlParseError(f"input {input_id} is missing from workflow job file") + if not isinstance(value, type_map[type_]): raise CwlParseError("Input/param types do not match: " - f"{input_id}/{self.params[input_id]}") - return self.params[input_id] + f"{input_id}/{value}") + return value workflow_name = os.path.basename(cwl_path).split(".")[0] workflow_inputs = {InputParameter(_shortname(input_.id), input_.type, @@ -245,6 +246,9 @@ def parse_step_outputs(cwl_out, step_outputs, stdout, stderr): :type stderr: str or None :rtype: list of StepOutput """ + if not cwl_out: + return [] + out_short = list(map(_shortname, cwl_out)) short_id = out_short[0].split("/")[0] # Inline step outputs already have short_id+"/" prepended @@ -291,6 +295,33 @@ def _read_requirement_file(self, key, items): except FileNotFoundError: msg = f'Could not find a file for {key}: {fname}' raise CwlParseError(msg) from None + if key in {'pre_script', 'post_script'}: + self._validate_prepost_shell_env(key, items, fname) + + def _validate_prepost_shell_env(self, key, items, fname): + """Validate defined shell interpreters. + + :param fname: name of pre/post script file + :type fname: str + """ + env_decl = items[key].splitlines() + # Need to remove whitespaces/newlines from list + env_decl = [x for x in env_decl if x.strip()] + # Check for shebang line in pre/post scripts + if not env_decl[0].startswith("#!"): + msg = f'No shebang line found in {fname}' + raise CwlParseError(msg) from None + # Now check for matching shell and shebang line values + shell_val = '#!' + items['shell'] + shebang_val = env_decl[0] + if shell_val != shebang_val: + msg = f'CWL file shell {shell_val} does not match {fname} shell {shebang_val}' + raise CwlParseError(msg) from None + # Remove shebang lines from scripts + rm_line = env_decl[1:] + # List to string format + rm_line = "\n".join(rm_line) + items.update({key: rm_line}) def parse_requirements(self, requirements, as_hints=False): """Parse CWL hints/requirements. @@ -316,10 +347,19 @@ def parse_requirements(self, requirements, as_hints=False): # Load in the dockerfile at parse time if 'dockerFile' in items: self._read_requirement_file('dockerFile', items) + # Load in pre/post scripts and make sure shell option is defined in cwl file if 'pre_script' in items and items['enabled']: - self._read_requirement_file('pre_script', items) + if 'shell' in items: + self._read_requirement_file('pre_script', items) + else: + msg = f'pre script enabled but shell option undefined in cwl file.' #noqa + raise CwlParseError(msg) from None if 'post_script' in items and items['enabled']: - self._read_requirement_file('post_script', items) + if 'shell' in items: + self._read_requirement_file('post_script', items) + else: + msg = f'post script enabled but shell option undefined in cwl file.' #noqa + raise CwlParseError(msg) from None if 'beeflow:bindMounts' in items: self._read_requirement_file('beeflow:bindMounts', items) reqs.append(Hint(req['class'], items)) diff --git a/beeflow/common/paths.py b/beeflow/common/paths.py index 1d3043c14..e6b7047ce 100644 --- a/beeflow/common/paths.py +++ b/beeflow/common/paths.py @@ -3,14 +3,14 @@ from beeflow.common.config_driver import BeeConfig as bc -def _workdir(): +def workdir(): """Return the workdir.""" return bc.get('DEFAULT', 'bee_workdir') def _sockdir(): """Return the socket directory.""" - sockdir = os.path.join(_workdir(), 'sockets') + sockdir = os.path.join(workdir(), 'sockets') os.makedirs(sockdir, exist_ok=True) return sockdir @@ -30,6 +30,11 @@ def tm_socket(): return os.path.join(_sockdir(), 'task_manager.sock') +def remote_socket(): + """Get the socket path for the Remote API.""" + return os.path.join(_sockdir(), 'remote.sock') + + def sched_socket(): """Get the scheduler socket.""" return os.path.join(_sockdir(), 'scheduler.sock') @@ -53,14 +58,14 @@ def log_fname(component): def redis_root(): """Get the redis root directory (create it if it doesn't exist).""" - path = os.path.join(_workdir(), 'redis') + path = os.path.join(workdir(), 'redis') os.makedirs(path, exist_ok=True) return path def redis_container(): """Get the path to the unpacked Redis container.""" - return os.path.join(_workdir(), 'redis_container') + return os.path.join(workdir(), 'deps/redis_container') def redis_sock_fname(): @@ -70,7 +75,7 @@ def redis_sock_fname(): def _celery_root(): """Get the celery root directory (create it if it doesn't exist).""" - path = os.path.join(_workdir(), 'celery') + path = os.path.join(workdir(), 'celery') os.makedirs(path, exist_ok=True) return path @@ -83,3 +88,9 @@ def celery_config(): def celery_db(): """Return the celery db path.""" return os.path.join(_celery_root(), 'celery.db') + + +def droppoint_root(): + """Get the root directory for the current droppoint.""" + bee_droppoint = bc.get('DEFAULT', 'bee_droppoint') + return bee_droppoint diff --git a/beeflow/common/wf_data.py b/beeflow/common/wf_data.py index 0761d8715..1777c339f 100644 --- a/beeflow/common/wf_data.py +++ b/beeflow/common/wf_data.py @@ -20,6 +20,9 @@ Requirement = namedtuple("Requirement", ["class_", "params"]) # CWL hint class Hint = namedtuple("Hint", ["class_", "params"]) +# Task state update, usually sent from the task manager +TaskStateUpdate = namedtuple("TaskStateUpdate", ["wf_id", "task_id", "job_state", + "task_info", "output", "metadata"]) def generate_workflow_id(): @@ -287,7 +290,10 @@ def command(self): nonpositional_inputs = [] for input_ in self.inputs: if input_.value is None: - raise ValueError("trying to construct command for task with missing input value") + raise ValueError( + ("trying to construct command for task with missing input value " + f"(id: {input_.id})") + ) if input_.position is not None: positional_inputs.append(input_) diff --git a/beeflow/common/wf_interface.py b/beeflow/common/wf_interface.py index d34a790d5..c6b1701cb 100644 --- a/beeflow/common/wf_interface.py +++ b/beeflow/common/wf_interface.py @@ -5,6 +5,7 @@ import re from beeflow.common import log as bee_logging +from beeflow.common.gdb.neo4j_driver import Neo4jDriver log = bee_logging.setup(__name__) @@ -12,7 +13,7 @@ class WorkflowInterface: """Interface for manipulating workflows.""" - def __init__(self, gdb_interface): + def __init__(self, wf_id, gdb_driver=Neo4jDriver): """Initialize the Workflow interface. Initializing this interface automatically attempts to @@ -21,13 +22,23 @@ def __init__(self, gdb_interface): :param gdb_interface: the gdb interface """ # Connect to the graph database - self._gdb_interface = gdb_interface - # Store the Workflow ID in the interface to assign it to new task objects - self._workflow_id = None + self._gdb_driver = gdb_driver + self._workflow_id = wf_id - def reconnect(self): - """Reconnect to the graph database using stored credentials.""" - raise NotImplementedError() + @property + def workflow_id(self): + """Retrieve the workflow ID from the workflow interface. + + If workflow ID is not populated, this grabs it from the database. + + If no workflow is loaded, None is returned. + :rtype: str + """ + if self._workflow_id is None: + workflow, _ = self.get_workflow() + self._workflow_id = workflow.id + + return self._workflow_id def initialize_workflow(self, workflow): """Begin construction of a BEE workflow. @@ -35,9 +46,6 @@ def initialize_workflow(self, workflow): :param workflow: the workflow object :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 = [] if workflow.hints is None: @@ -45,32 +53,27 @@ def initialize_workflow(self, workflow): self._workflow_id = workflow.id # Load the new workflow into the graph database - self._gdb_interface.initialize_workflow(workflow) + self._gdb_driver.initialize_workflow(workflow) def execute_workflow(self): """Begin execution of a BEE workflow.""" - self._gdb_interface.execute_workflow() + self._gdb_driver.execute_workflow(self._workflow_id) def pause_workflow(self): """Pause the execution of a BEE workflow.""" - self._gdb_interface.pause_workflow() + self._gdb_driver.pause_workflow(self._workflow_id) def resume_workflow(self): """Resume the execution of a paused BEE workflow.""" - self._gdb_interface.resume_workflow() + self._gdb_driver.resume_workflow(self._workflow_id) def reset_workflow(self, workflow_id): """Reset the execution state and ID of a BEE workflow.""" + self._gdb_driver.reset_workflow(self._workflow_id, workflow_id) self._workflow_id = workflow_id - self._gdb_interface.reset_workflow(self._workflow_id) - self._gdb_interface.set_workflow_state('SUBMITTED') - - def finalize_workflow(self): - """Deconstruct a BEE workflow.""" - self._workflow_id = None - self._gdb_interface.cleanup() + self._gdb_driver.set_workflow_state(self._workflow_id, 'SUBMITTED') - def add_task(self, task): + def add_task(self, task, task_state): """Add a new task to a BEE workflow. :param task: the name of the file to which to redirect stderr @@ -87,7 +90,7 @@ def add_task(self, task): task.hints = [] # Load the new task into the graph database - self._gdb_interface.load_task(task) + self._gdb_driver.load_task(task, task_state) def restart_task(self, task, checkpoint_file): """Restart a failed BEE workflow task. @@ -125,7 +128,7 @@ def restart_task(self, task, checkpoint_file): i = int(match.group(1)) new_task.name = re.sub(r"\([0-9]+\)", f"({i + 1})", new_task.name) metadata = self.get_task_metadata(task) - self._gdb_interface.restart_task(task, new_task) + self._gdb_driver.restart_task(task, new_task) self.set_task_metadata(new_task, metadata) self.set_task_state(task, "RESTARTED") self.set_task_state(new_task, "READY") @@ -142,9 +145,9 @@ def finalize_task(self, task): :type task: Task :rtype: list of Task """ - self._gdb_interface.finalize_task(task) - self._gdb_interface.initialize_ready_tasks() - return self._gdb_interface.get_ready_tasks() + self._gdb_driver.finalize_task(task) + self._gdb_driver.initialize_ready_tasks(self._workflow_id) + return self._gdb_driver.get_ready_tasks(self._workflow_id) def get_task_by_id(self, task_id): """Get a task by its Task ID. @@ -153,7 +156,7 @@ def get_task_by_id(self, task_id): :type task_id: str :rtype: Task """ - return self._gdb_interface.get_task_by_id(task_id) + return self._gdb_driver.get_task_by_id(task_id) def get_workflow(self): """Get a loaded BEE workflow. @@ -162,8 +165,8 @@ def get_workflow(self): :rtype: tuple of (Workflow, list of Task) """ - workflow = self._gdb_interface.get_workflow_description() - tasks = self._gdb_interface.get_workflow_tasks() + workflow = self._gdb_driver.get_workflow_description(self._workflow_id) + tasks = self._gdb_driver.get_workflow_tasks(self._workflow_id) return workflow, tasks def get_workflow_outputs(self): @@ -171,7 +174,7 @@ def get_workflow_outputs(self): :rtype: list of OutputParameter """ - workflow = self._gdb_interface.get_workflow_description() + workflow = self._gdb_driver.get_workflow_description(self._workflow_id) return workflow.outputs def get_workflow_state(self): @@ -179,23 +182,23 @@ def get_workflow_state(self): :rtype: str """ - state = self._gdb_interface.get_workflow_state() + state = self._gdb_driver.get_workflow_state(self._workflow_id) return state def set_workflow_state(self, state): - """Return workflow's current state. + """Set workflow's current state. :param state: the new state of the workflow :type state: str """ - self._gdb_interface.set_workflow_state(state) + self._gdb_driver.set_workflow_state(self._workflow_id, state) def get_ready_tasks(self): """Get ready tasks from a BEE workflow. :rtype: list of Task """ - return self._gdb_interface.get_ready_tasks() + return self._gdb_driver.get_ready_tasks(self._workflow_id) def get_dependent_tasks(self, task): """Get the dependents of a task in a BEE workflow. @@ -204,7 +207,7 @@ def get_dependent_tasks(self, task): :type task: Task :rtype: list of Task """ - return self._gdb_interface.get_dependent_tasks(task) + return self._gdb_driver.get_dependent_tasks(task) def get_task_state(self, task): """Get the state of the task in a BEE workflow. @@ -213,7 +216,7 @@ def get_task_state(self, task): :type task: Task :rtype: str """ - return self._gdb_interface.get_task_state(task) + return self._gdb_driver.get_task_state(task) def set_task_state(self, task, state): """Set the state of the task in a BEE workflow. @@ -226,7 +229,7 @@ def set_task_state(self, task, state): :param state: the new state of the task :type state: str """ - self._gdb_interface.set_task_state(task, state) + self._gdb_driver.set_task_state(task, state) def get_task_metadata(self, task): """Get the job description metadata of a task in a BEE workflow. @@ -235,7 +238,7 @@ def get_task_metadata(self, task): :type task: Task :rtype: dict """ - return self._gdb_interface.get_task_metadata(task) + return self._gdb_driver.get_task_metadata(task) def set_task_metadata(self, task, metadata): """Set the job description metadata of a task in a BEE workflow. @@ -248,7 +251,7 @@ def set_task_metadata(self, task, metadata): :param metadata: the job description metadata :type metadata: dict """ - self._gdb_interface.set_task_metadata(task, metadata) + self._gdb_driver.set_task_metadata(task, metadata) def get_task_input(self, task, input_id): """Get a task input object. @@ -259,7 +262,7 @@ def get_task_input(self, task, input_id): :type input_id: str :rtype: StepInput """ - return self._gdb_interface.get_task_input(task, input_id) + return self._gdb_driver.get_task_input(task, input_id) def set_task_input(self, task, input_id, value): """Set the value of a task input. @@ -270,7 +273,7 @@ def set_task_input(self, task, input_id, value): :type input_id: str :param value: str or int or float """ - self._gdb_interface.set_task_input(task, input_id, value) + self._gdb_driver.set_task_input(task, input_id, value) def get_task_output(self, task, output_id): """Get a task output object. @@ -281,7 +284,7 @@ def get_task_output(self, task, output_id): :type output_id: str :rtype: StepOutput """ - return self._gdb_interface.get_task_output(task, output_id) + return self._gdb_driver.get_task_output(task, output_id) def set_task_output(self, task, output_id, value): """Set the value of a task output. @@ -293,60 +296,15 @@ def set_task_output(self, task, output_id, value): :param value: the output value to set :type value: str or int or float """ - self._gdb_interface.set_task_output(task, output_id, value) - - def evaluate_expression(self, task, id_, output=False): - """Evaluate a task input/output expression. - - Expression can be either a string concatenation in a StepInput - valueFrom field or a parameter substitution in a StepOutput - glob field. The only special variable supported in valueFrom is - self.path. - - :param task: the task whose expression to evaluate - :type task: Task - :param id_: the id of the step input/output - :type id_: str - :param output: true if output glob expression being evaluated, else false - :type output: bool - """ - self._gdb_interface.evaluate_expression(task, id_, output) + self._gdb_driver.set_task_output(task, output_id, value) def workflow_completed(self): """Return true if all of a workflow's final tasks have completed, else false. :rtype: bool """ - return self._gdb_interface.workflow_completed() - - def workflow_initialized(self): - """Return true if a workflow has been initialized, else false. - - Currently functionally the same as workflow_loaded() but may - change when multiple workflows per database instance are supported. + return self._gdb_driver.workflow_completed(self._workflow_id) - :rtype: bool - """ - return self._gdb_interface.initialized() - - def workflow_loaded(self): - """Return true if a workflow is loaded, else false. - - :rtype: bool - """ - return bool(not self._gdb_interface.empty()) - - @property - def workflow_id(self): - """Retrieve the workflow ID from the workflow interface. - - If workflow ID is not populated, this grabs it from the database. - - If no workflow is loaded, None is returned. - :rtype: str - """ - if self._workflow_id is None and self.workflow_loaded(): - workflow, _ = self.get_workflow() - self._workflow_id = workflow.id - - return 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/common/worker/__init__.py b/beeflow/common/worker/__init__.py index 6e7d4ffd8..4afc064d1 100644 --- a/beeflow/common/worker/__init__.py +++ b/beeflow/common/worker/__init__.py @@ -1,5 +1,6 @@ """Init file for the worker package.""" +from beeflow.common.worker.worker import WorkerError # noqa: this is imported for external code from beeflow.common.worker.slurm_worker import SlurmWorker from beeflow.common.worker.lsf_worker import LSFWorker from beeflow.common.worker.flux_worker import FluxWorker diff --git a/beeflow/common/worker/flux_worker.py b/beeflow/common/worker/flux_worker.py index 353f38214..98624f052 100644 --- a/beeflow/common/worker/flux_worker.py +++ b/beeflow/common/worker/flux_worker.py @@ -1,5 +1,6 @@ """Flux worker interface.""" +import io import os from beeflow.common import log as bee_logging from beeflow.common.worker.worker import Worker @@ -42,12 +43,15 @@ def build_jobspec(self, task): """Build the job spec for a task.""" # TODO: This has a lot of code in common with the other worker's build_text crt_res = self.crt.run_text(task) + shell = task.get_requirement('beeflow:ScriptRequirement', 'shell', default='/bin/bash') script = [ - '#!/bin/bash', - 'set -e', - crt_res.env_code, + f'#!{shell}', ] + if shell == "/bin/bash": + script.append('set -e') + script.append(crt_res.env_code) + # TODO: Should this entire model, saving stdout and stderr to files, be # redone for Flux? It seems to provide some sort of KVS for storing # output but I don't quite understand it. @@ -59,6 +63,19 @@ def build_jobspec(self, task): # TODO: What to do with the MPI version? # mpi_version = task.get_requirement('beeflow:MPIRequirement', 'mpiVersion', # default='pmi2') + scripts_enabled = task.get_requirement('beeflow:ScriptRequirement', 'enabled', + default=False) + if scripts_enabled: + # We use StringIO here to properly break the script up into lines with readlines + pre_script = io.StringIO(task.get_requirement('beeflow:ScriptRequirement', + 'pre_script')).readlines() + post_script = io.StringIO(task.get_requirement('beeflow:ScriptRequirement', + 'post_script')).readlines() + + # Pre commands + if scripts_enabled: + for cmd in pre_script: + script.append(cmd) for cmd in crt_res.pre_commands: if cmd.type == 'one-per-node': @@ -67,7 +84,7 @@ def build_jobspec(self, task): cmd_args = ['flux', 'run', ' '.join(cmd.args)] script.append(' '.join(cmd_args)) - # Set up the main command + # Main command args = ['flux', 'run', '-N', str(nodes), '-n', str(ntasks)] if task.stdout is not None: args.extend(['--output', task.stdout]) @@ -77,6 +94,7 @@ def build_jobspec(self, task): log.info(args) script.append(' '.join(args)) + # Post commands for cmd in crt_res.post_commands: if cmd.type == 'one-per-node': cmd_args = ['flux', 'run', '-N', str(nodes), '-n', str(nodes), ' '.join(cmd.args)] @@ -84,6 +102,10 @@ def build_jobspec(self, task): cmd_args = ['flux', 'run', ' '.join(cmd.args)] script.append(' '.join(cmd_args)) + if scripts_enabled: + for cmd in post_script: + script.append(cmd) + script = '\n'.join(script) jobspec = self.job.JobspecV1.from_batch_command(script, task.name, num_slots=ntasks, @@ -93,8 +115,8 @@ def build_jobspec(self, task): jobspec.stderr = f'{task_save_path}/{task.name}-{task.id}.err' jobspec.environment = dict(os.environ) # Save the script for later reference - with open(f'{task_save_path}/{task.name}-{task.id}.sh', 'w', encoding='utf-8') as fp: - fp.write(script) + with open(f'{task_save_path}/{task.name}-{task.id}.sh', 'w', encoding='utf-8') as f_path: + f_path.write(script) return jobspec def submit_task(self, task): diff --git a/beeflow/common/worker/slurm_worker.py b/beeflow/common/worker/slurm_worker.py index d182521a4..b8bc6207d 100644 --- a/beeflow/common/worker/slurm_worker.py +++ b/beeflow/common/worker/slurm_worker.py @@ -14,6 +14,9 @@ from beeflow.common import log as bee_logging from beeflow.common.worker.worker import (Worker, WorkerError) from beeflow.common import validation +from beeflow.common.worker.utils import get_state_sacct +from beeflow.common.worker.utils import parse_key_val + log = bee_logging.setup(__name__) @@ -44,7 +47,8 @@ def build_text(self, task): main_command_srun_args = [] nodes = task.get_requirement('beeflow:MPIRequirement', 'nodes', default=1) ntasks = task.get_requirement('beeflow:MPIRequirement', 'ntasks', default=nodes) - mpi_version = task.get_requirement('beeflow:MPIRequirement', 'mpiVersion', default='pmi2') + # Need to rethink the MPI version parameter + mpi_version = task.get_requirement('beeflow:MPIRequirement', 'mpiVersion', default='') time_limit = task.get_requirement('beeflow:SchedulerRequirement', 'timeLimit', default=self.default_time_limit) time_limit = validation.time_limit(time_limit) @@ -54,6 +58,7 @@ def build_text(self, task): 'partition', default=self.default_partition) + shell = task.get_requirement('beeflow:ScriptRequirement', 'shell', default="/bin/bash") scripts_enabled = task.get_requirement('beeflow:ScriptRequirement', 'enabled', default=False) if scripts_enabled: @@ -64,7 +69,7 @@ def build_text(self, task): 'post_script')).readlines() # sbatch header script = [ - '#!/bin/bash', + f'#!{shell}', f'#SBATCH --job-name={task.name}-{task.id}', f'#SBATCH --output={task_save_path}/{task.name}-{task.id}.out', f'#SBATCH --error={task_save_path}/{task.name}-{task.id}.err', @@ -80,7 +85,8 @@ def build_text(self, task): script.append(f'#SBATCH -p {partition}') # Return immediately on error - script.append('set -e') + if shell == "/bin/bash": + script.append('set -e') script.append(crt_res.env_code) def srun(script_lines, script_cmd): @@ -102,7 +108,11 @@ def srun(script_lines, script_cmd): # Main command srun_args = ' '.join(main_command_srun_args) args = ' '.join(crt_res.main_command.args) - script.append(f'srun --mpi={mpi_version} {srun_args} {args}') + if mpi_version: + mpi_arg = f'--mpi={mpi_version}' + else: + mpi_arg = '' + script.append(f'srun --nodes={nodes} {mpi_arg} {srun_args} {args}') # Post commands for cmd in crt_res.post_commands: @@ -160,17 +170,18 @@ def query_task(self, job_id): """Worker queries job; returns job_state.""" try: resp = self.session.get(f'{self.slurm_url}/job/{job_id}') - - if resp.status_code != 200: - raise WorkerError(f'Failed to query job {job_id}') - data = json.loads(resp.text) - # Check for errors in the response - check_slurm_error(data, f'Failed to query job {job_id}') - # For some versions of slurm, the job_state isn't included on failure - try: - job_state = data['jobs'][0]['job_state'] - except (KeyError, IndexError) as exc: - raise WorkerError(f'Failed to query job {job_id}') from exc + if resp.status_code == 200: + data = json.loads(resp.text) + # Check for errors in the response + check_slurm_error(data, f'Failed to query job {job_id}, slurm error.') + # For some versions of slurm, the job_state isn't included on failure + try: + job_state = data['jobs'][0]['job_state'] + except (KeyError, IndexError) as exc: + raise WorkerError(f'Failed to query job {job_id}') from exc + else: + # If slurmrestd does not find job make last attempt with sacct command + job_state = get_state_sacct(job_id) except requests.exceptions.ConnectionError: job_state = "NOT_RESPONDING" return job_state @@ -200,24 +211,19 @@ class SlurmCLIWorker(BaseSlurmWorker): def query_task(self, job_id): """Query job state for the task.""" - # Use scontrol since it gives a lot of useful info + # Use scontrol since it gives a lot of useful info; may want to save info try: res = subprocess.run(['scontrol', 'show', 'job', str(job_id)], text=True, check=True, stdout=subprocess.PIPE) except subprocess.CalledProcessError: - raise WorkerError( - f'Failed to query job {job_id}' - ) from None - - def parse_key_val(pair): - """Parse the key-value pair.""" - i = pair.find('=') - return (pair[:i], pair[i + 1:]) - - # Output is in a space-separated list of 'key=value' pairs - pairs = res.stdout.split() - key_vals = dict(parse_key_val(pair) for pair in pairs) - return key_vals['JobState'] + # If show job cannot find job get state using sacct (not same info) + job_state = get_state_sacct(job_id) + else: + # Output is in a space-separated list of 'key=value' pairs + pairs = res.stdout.split() + key_vals = dict(parse_key_val(pair) for pair in pairs) + job_state = key_vals['JobState'] + return job_state def cancel_task(self, job_id): """Cancel task with job_id; returns job_state.""" diff --git a/beeflow/common/worker/utils.py b/beeflow/common/worker/utils.py new file mode 100644 index 000000000..ab019fa4e --- /dev/null +++ b/beeflow/common/worker/utils.py @@ -0,0 +1,34 @@ +"""Worker utility functions.""" + +import subprocess +from beeflow.common.worker.worker import WorkerError +from beeflow.common import log as bee_logging + + +log = bee_logging.setup(__name__) + + +def get_state_sacct(job_id): + """Get state from slurm using sacct command, used when other means fail.""" + log.info(f'Getting state with sacct for {job_id}') + try: + job_id = str(job_id) + resp = subprocess.run(['sacct', '--parsable', '-j', job_id], text=True, check=True, + stdout=subprocess.PIPE) + data = resp.stdout.splitlines() + header = data[0] + header = header.split('|') + job_id_idx = header.index('JobID') + rows = [row.split('|') for row in data[1:]] + job_ids = [row[job_id_idx] for row in rows] + info = rows[job_ids.index(job_id)] + state_idx = header.index('State') + return info[state_idx] + except (subprocess.CalledProcessError, ValueError, KeyError) as exc: + raise WorkerError(f'sacct query failed for job {job_id}') from exc + + +def parse_key_val(pair): + """Parse the key-value pair separated by '='.""" + i = pair.find('=') + return (pair[:i], pair[i + 1:]) diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/clamr_wf.cwl b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/clamr_wf.cwl index fd8ffac5a..13baf637c 100644 --- a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/clamr_wf.cwl +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/clamr_wf.cwl @@ -54,6 +54,7 @@ steps: enabled: true pre_script: "pre_run.sh" post_script: "post_run.sh" + shell: "/bin/bash" DockerRequirement: dockerFile: "Dockerfile.clamr-ffmpeg" beeflow:containerName: "clamr-ffmpeg" diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/post_run.sh b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/post_run.sh index e4eb7f6c9..c6bcfafaa 100644 --- a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/post_run.sh +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/post_run.sh @@ -1 +1,3 @@ +#!/bin/bash + echo "After run" diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/pre_run.sh b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/pre_run.sh index dd7e00efc..035ffa7de 100644 --- a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/pre_run.sh +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-build_script/pre_run.sh @@ -1 +1,3 @@ +#!/bin/bash + echo "Before run" diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/Dockerfile.clamr-ffmpeg b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/Dockerfile.clamr-ffmpeg new file mode 100644 index 000000000..be993ba18 --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/Dockerfile.clamr-ffmpeg @@ -0,0 +1,12 @@ +# Dockerfile.clamr-ffmpeg +# Developed on Chicoma @lanl +# Patricia Grubel + +FROM debian:11 + + +RUN apt-get update && \ + apt-get install -y wget gnupg git cmake ffmpeg g++ make openmpi-bin libopenmpi-dev libpng-dev libpng16-16 libpng-tools imagemagick libmagickwand-6.q16-6 libmagickwand-6.q16-dev + +RUN git clone https://github.com/lanl/CLAMR.git +RUN cd CLAMR && cmake . && make clamr_cpuonly diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/README.md b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/README.md new file mode 100644 index 000000000..fa729805c --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/README.md @@ -0,0 +1,13 @@ +# CLAMR - FFMPEG workflow using CWL + +This workflow uses the DockerRequirements dockerFile and beeflow:containerNameto build the clamr and ffmpeg in a container. + +``` +clamr_wf.cwl - the main cwl +calmr_job.yml - yaml file for values used by the cwl files +clamr.cwl - cwl file for the clamr step +ffmpeg.cwl - cwl file for the ffmpeg step +``` + + + diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr.cwl b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr.cwl new file mode 100644 index 000000000..1ee7aa297 --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr.cwl @@ -0,0 +1,72 @@ +# -*- mode: YAML; -*- + +class: CommandLineTool +cwlVersion: v1.0 + +baseCommand: /CLAMR/clamr_cpuonly +# This is the stdout field which makes all stdout be captured in this file +stdout: clamr_stdout.txt +# Arguments to the command +inputs: + amr_type: + # ? means the argument is optional + # All of the ? here are legacy from the original CWL + type: string? + # Declare extra options + # We support prefix and position + inputBinding: + # Prefix is the flag for cli command + prefix: -A + grid_res: + type: int? + inputBinding: + prefix: -n + max_levels: + type: int? + inputBinding: + prefix: -l + time_steps: + type: int? + inputBinding: + prefix: -t + output_steps: + type: int? + inputBinding: + prefix: -i + graphic_steps: + type: int? + inputBinding: + prefix: -g + graphics_type: + type: string? + inputBinding: + prefix: -G + rollback_images: + type: int? + inputBinding: + prefix: -b + checkpoint_disk_interval: + type: int? + inputBinding: + prefix: -c + checkpoint_mem_interval: + type: int? + inputBinding: + prefix: -C + hash_method: + type: string? + inputBinding: + prefix: -e + +outputs: + # Captures stdout. Name is arbitrary. + clamr_stdout: + type: stdout + outdir: + type: Directory + outputBinding: + glob: graphics_output/graph%05d.png + time_log: + type: File + outputBinding: + glob: total_execution_time.log diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_job.json b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_job.json new file mode 100644 index 000000000..ad88972f6 --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_job.json @@ -0,0 +1,13 @@ +{ + "grid_resolution": 32, + "max_levels": 3, + "time_steps": 5000, + "steps_between_outputs": 10, + "steps_between_graphics": 25, + "graphics_type": "png", + "input_format": "image2", + "frame_rate": 12, + "frame_size": "800x800", + "pixel_format": "yuv420p", + "output_filename": "CLAMR_movie.mp4" +} diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_job.yml b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_job.yml new file mode 100644 index 000000000..e20e6470b --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_job.yml @@ -0,0 +1,18 @@ +# Inputs for CLAMR +# /CLAMR/clamr_cpuonly -n 32 -l 3 -t 5000 -i 10 -g 25 -G png + +grid_resolution: 32 +max_levels: 3 +time_steps: 5000 +steps_between_outputs: 10 +steps_between_graphics: 25 +graphics_type: png + +# Inputs for FFMPEG +#ffmpeg -f image2 -r 12 -s 800x800 -pix_fmt yuv420p CLAMR_movie.mp4 + +input_format: image2 +frame_rate: 12 +frame_size: 800x800 +pixel_format: yuv420p +output_filename: CLAMR_movie.mp4 diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_wf.cwl b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_wf.cwl new file mode 100644 index 000000000..13baf637c --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_wf.cwl @@ -0,0 +1,79 @@ +# -*- mode: YAML; -*- + +class: Workflow +cwlVersion: v1.0 + +# Main 3 components of workflow are inputs, outputs, and steps + +inputs: +# All inputs go here for each step. No way to break them up. +# We should talk to the CWL people about that. +##### CLAMR inputs ##### +# takes ID:Type syntax + grid_resolution: int + max_levels: int + time_steps: int + steps_between_outputs: int + steps_between_graphics: int + graphics_type: string +##### FFMPEG inputs ##### + input_format: string + frame_rate: int + frame_size: string + pixel_format: string + output_filename: string + +outputs: +# Outputs for all the steps + clamr_stdout: + type: File + outputSource: clamr/clamr_stdout + clamr_time_log: + type: File + outputSource: clamr/time_log + clamr_movie: + type: File + outputSource: ffmpeg/movie + ffmpeg_stderr: + type: File + outputSource: ffmpeg/ffmpeg_stderr + +steps: + clamr: + run: clamr.cwl + in: + grid_res: grid_resolution + max_levels: max_levels + time_steps: time_steps + output_steps: steps_between_outputs + graphic_steps: steps_between_graphics + graphics_type: graphics_type + out: [clamr_stdout, outdir, time_log] + hints: + beeflow:ScriptRequirement: + enabled: true + pre_script: "pre_run.sh" + post_script: "post_run.sh" + shell: "/bin/bash" + DockerRequirement: + dockerFile: "Dockerfile.clamr-ffmpeg" + beeflow:containerName: "clamr-ffmpeg" + + ffmpeg: + run: ffmpeg.cwl + in: + input_format: input_format + # input syntax is name: /dependent_object + ffmpeg_input: clamr/outdir + frame_rate: frame_rate + frame_size: frame_size + pixel_format: pixel_format + # Setting output file with file_name + # output_filename set in wf inputs + output_file: output_filename + # Multiple outputs can be in array + out: [movie, ffmpeg_stderr] + hints: + DockerRequirement: + dockerFile: "Dockerfile.clamr-ffmpeg" + beeflow:containerName: "clamr-ffmpeg" diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/ffmpeg.cwl b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/ffmpeg.cwl new file mode 100644 index 000000000..bd9f27513 --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/ffmpeg.cwl @@ -0,0 +1,49 @@ +# -*- mode: YAML; -*- + +class: CommandLineTool +cwlVersion: v1.0 + +baseCommand: ffmpeg -y + +stderr: ffmpeg_stderr.txt + +inputs: + input_format: + type: string? + inputBinding: + prefix: -f + position: 1 + ffmpeg_input: + type: Directory + inputBinding: + prefix: -i + position: 2 + valueFrom: $("/graph%05d.png") + frame_rate: + type: int? + inputBinding: + prefix: -r + position: 3 + frame_size: + type: string? + inputBinding: + prefix: -s + position: 4 + pixel_format: + type: string? + inputBinding: + prefix: -pix_fmt + position: 5 + output_file: + type: string + inputBinding: + position: 6 + +outputs: + movie: + type: File + outputBinding: + glob: $(inputs.output_file) + # glob: CLAMR_movie.mp4 + ffmpeg_stderr: + type: stderr diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/post_run.sh b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/post_run.sh new file mode 100644 index 000000000..e4eb7f6c9 --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/post_run.sh @@ -0,0 +1 @@ +echo "After run" diff --git a/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/pre_run.sh b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/pre_run.sh new file mode 100644 index 000000000..dd7e00efc --- /dev/null +++ b/beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/pre_run.sh @@ -0,0 +1 @@ +echo "Before run" diff --git a/beeflow/enhanced_client/README.rst b/beeflow/enhanced_client/README.rst deleted file mode 100644 index 15535d556..000000000 --- a/beeflow/enhanced_client/README.rst +++ /dev/null @@ -1,14 +0,0 @@ -Enhanced BEE Client Installation Instructions ---------------------------------------------- - -First install ``nvm`` from `here -`_. This is a node.js -package manager. - -Next, you can install dependencies with ``npm install``. If you are running on a -VPN or you're traffic is directed through a proxy, you will need to temporarily -turn it off and unset the proxy environment variables (``http_proxy``, -``https_proxy``, ``HTTP_PROXY``, ``HTTPS_PROXY``). - -Finally, start the app with ``npm start``. This can be done with the VPN and -proxy on, since all packages should already be installed. diff --git a/beeflow/enhanced_client/data/.gitkeep b/beeflow/enhanced_client/data/.gitkeep deleted file mode 100644 index e69de29bb..000000000 diff --git a/beeflow/enhanced_client/forge.config.js b/beeflow/enhanced_client/forge.config.js deleted file mode 100644 index 9a4060f97..000000000 --- a/beeflow/enhanced_client/forge.config.js +++ /dev/null @@ -1,22 +0,0 @@ -module.exports = { - packagerConfig: {}, - rebuildConfig: {}, - makers: [ - { - name: '@electron-forge/maker-squirrel', - config: {}, - }, - { - name: '@electron-forge/maker-zip', - platforms: ['darwin'], - }, - { - name: '@electron-forge/maker-deb', - config: {}, - }, - { - name: '@electron-forge/maker-rpm', - config: {}, - }, - ], -}; diff --git a/beeflow/enhanced_client/main.js b/beeflow/enhanced_client/main.js deleted file mode 100644 index 1f6a67134..000000000 --- a/beeflow/enhanced_client/main.js +++ /dev/null @@ -1,60 +0,0 @@ -// Modules -const {app, BrowserWindow, ipcMain} = require('electron') - -app.allowRendererProcessReuse = true - -// Used to handle error in MacOS systems -if (app.getGPUFeatureStatus().gpu_compositing.includes("disabled")) { - app.disableHardwareAcceleration(); -} - -// Need global reference to window object so it doesn't -// get garbage collected and close the window -let mainWindow; - -// Creates the main application window -function createWindow () { - mainWindow = new BrowserWindow({ - // TODO Change width and height so it's proportionl to the screen size - width: 1400, height: 1000, - webPreferences: { - // App needs to be modified so these can be changed to true and false - contextIsolation: false, - nodeIntegration: true, - webSecurity: false, - experimentalFeatures: true - } - }) - - // Load main.html into the new BrowserWindow - mainWindow.loadFile('renderer/main.html') - - // Open DevTools - mainWindow.webContents.openDevTools(); - - // Listen for window being closed - mainWindow.on('closed', () => { - mainWindow = null - }) -} - -// Create app window when ready -app.on('ready', createWindow) - -// Close application when all windows are closed unless on macOS -app.on('window-all-closed', () => { - if (process.platform !== 'darwin') app.quit() -}) - -// When app icon is clicked and app is running, (macOS) recreate the BrowserWindow -app.on('activate', () => { - if (mainWindow === null) createWindow() -}) - -// Will be used to recieve database update messages from renderer when -// nodeIntegration is disabled -// ipcMain.handle('db-add', async (event, arg) => { -// // Add data to DB -// await awaitableProcess(); -// return "Added"; -// }) diff --git a/beeflow/enhanced_client/package-lock.json b/beeflow/enhanced_client/package-lock.json deleted file mode 100644 index 087d99512..000000000 --- a/beeflow/enhanced_client/package-lock.json +++ /dev/null @@ -1,6394 +0,0 @@ -{ - "name": "BEEClient", - "version": "1.0.0", - "lockfileVersion": 3, - "requires": true, - "packages": { - "": { - "name": "BEEClient", - "version": "1.0.0", - "dependencies": { - "axios": "^1.6.0", - "bulma": "^0.9.3", - 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"node": ">=10" - }, - "funding": { - "url": "https://github.com/sponsors/sindresorhus" - } - } - } -} diff --git a/beeflow/enhanced_client/package.json b/beeflow/enhanced_client/package.json deleted file mode 100644 index 90094f521..000000000 --- a/beeflow/enhanced_client/package.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "name": "BEEViz", - "description": "Visualiztion client for the BEE workflow manager.", - "version": "1.0.0", - "main": "main.js", - "scripts": { - "start": "electron-forge start", - "watch": "nodemon --exec electron .", - "reset": "git reset --hard", - "pack": "electron-builder --dir", - "dist": "electron-builder", - "package": "electron-forge package", - "make": "electron-forge make" - }, - "repository": "https://github.com/lanl/BEE_Private", - "keywords": [ - "Workflows" - ], - "author": "BEE Team", - "devDependencies": { - "@electron-forge/cli": "^6.0.5", - "@electron-forge/maker-deb": "^6.0.5", - "@electron-forge/maker-rpm": "^6.0.5", - "@electron-forge/maker-squirrel": "^6.0.5", - "@electron-forge/maker-zip": "^6.0.5", - "electron": "^22.3.25", - "electron-rebuild": "^3.2.9" - }, - "dependencies": { - "axios": "^1.6.0", - "bulma": "^0.9.3", - "electron-squirrel-startup": "^1.0.0", - "form-data": "^4.0.0", - "idb": "^7.1.1", - "neo4j-driver": "^4.4.1", - "neovis.js": "^2.0.2", - "tunnel-ssh": "^4.1.6" - } -} diff --git a/beeflow/enhanced_client/renderer/app.js b/beeflow/enhanced_client/renderer/app.js deleted file mode 100644 index 3d649b6e1..000000000 --- a/beeflow/enhanced_client/renderer/app.js +++ /dev/null @@ -1,34 +0,0 @@ -// Renderer script and main app script - -// Helper function for showing messages in the page sidebar -function showMessage(containerId, className, message) { - let div = document.createElement('div'); - div.className = className; - // Button to remove old messages - let deleteButton = document.createElement('button'); - deleteButton.className = 'delete'; - deleteButton.addEventListener('click', ev => { - div.remove(); - }); - div.appendChild(deleteButton); - div.appendChild(document.createTextNode(message)); - // Add it to the container - let container = document.getElementById(containerId); - container.appendChild(div); - return div; -} - -const control = require('./control.js'); -control.setup({ - showErrorMessage: (message) => showMessage('messages', 'notification is-danger mb-4', message), - showMessage: (message) => showMessage('messages', 'notification is-primary mb-4', message), - hostname: 'settings-hostname', - hostnameError: 'settings-hostname-error', - moniker: 'settings-moniker', - monikerError: 'settings-moniker-error', - boltPort: 'settings-bolt_port', - boltPortError: 'settings-bolt_port-error', - submitButton: 'settings-submit', - reloadButton: 'reload-button', - vizContainer: 'viz', -}); diff --git a/beeflow/enhanced_client/renderer/client.js b/beeflow/enhanced_client/renderer/client.js deleted file mode 100644 index cfad74d8c..000000000 --- a/beeflow/enhanced_client/renderer/client.js +++ /dev/null @@ -1,178 +0,0 @@ -const http = require('http'); -const FormData = require('form-data'); -const axios = require('axios'); -const Path = require('path'); -const fs = require('fs'); -const config = require('./config.js'); - -const workflow_manager = 'bee_wfm/v1/jobs'; - -// TODO: When some sort of error occurs, most of these functions just log it to -// the console and then open an alert dialog. This would be better handled in -// the calling code with a .catch(). - -function _url() { - wfm_listen_port = 9999; - return `http://127.0.0.1:${wfm_listen_port}/${workflow_manager}/`; -} - -function _resource(tag='') { - return _url() + tag; -} - -// Build a request config with some useful defaults -function _build_config(method, url, data = null) { - let headers = { - 'Authorization': 'Bearer ...', - }; - if (data !== null) { - Object.assign(headers, data.getHeaders()); - } - return { - method, - url, - headers, - adapter: require('axios/lib/adapters/http'), - data, - // Just in case 'no_proxy' is set incorrectly - proxy: false, - }; -} - -function start_workflow(wf_id) { - return axios.post(_resource(wf_id)) - .then(resp => resp.data) - .catch(error => { - console.log(error); - alert("WFM communication failed"); - }); -} - -async function submit_workflow(workflow) { - var data = new FormData(); - data.append('workflow_archive', fs.createReadStream(workflow.tarball_path)); - data.append('wf_filename', workflow.tarball_fname); - data.append('main_cwl', workflow.main_cwl); - data.append('yaml', workflow.yaml); - data.append('workdir', workflow.workdir); - data.append('wf_name', workflow.name); - - let config = _build_config('post', _resource(workflow.wf_id), data) - return axios(config) - .then(response => { - console.log(JSON.stringify(response.data)); - process.stdout.write(JSON.stringify(response.data)); - // Get wf_id - wf_id = response.data['wf_id'] - // Get task information from response - tasks = response.data['tasks']; - return {wf_id, tasks}; - }) - .catch(error => { - console.log("Failed to communicate with WFM"); - console.log(error); - // TODO: Is there a log where this data can be saved? - alert("WFM communication failed"); - }); -} - -async function reexecute_workflow(workflow) { - var data = new FormData(); - data.append('name', workflow.name); - data.append('workflow_archive', fs.createReadStream(workflow.tarball_path)); - - let config = _build_config('put', _url(), data); - return axios(config) - .then(function (response) { - console.log(JSON.stringify(response.data)); - process.stdout.write(JSON.stringify(response.data)); - // Get wf_id - wf_id = response.data['wf_id'] - // Get task information from response - tasks = response.data['tasks']; - return {wf_id, tasks}; - }) - .catch(function (error) { - alert('Re-execute failed, there could be a connection problem'); - console.log(error); - }); -} - -// Query the current state of a workflow's task. -async function query_workflow(wf_id) { - let config = _build_config('get', _resource(wf_id)); - return axios(config) - .then(function (response) { - console.log(JSON.stringify(response.data)); - tasks = response.data['tasks']; - wf_status = response.data['wf']; - return {wf_status, tasks}; - }) - .catch(function (error) { - alert('Workflow query failed, there could be a connection problem'); - console.log(error); - }); -} - -function cancel_workflow(wf_id) { - return axios({ - method: 'delete', - url: _resource(wf_id), - proxy: false, - }).then(function (response) { - console.log(response.data); - }).catch(function (error) { - console.log(error); - }); -} - -// Need to think about making this async -function pause_workflow(wf_id) { - let config = _build_config('patch', _resource(wf_id), {option: 'pause'}); - - return axios(config) - .then(function (response) { - console.log(JSON.stringify(response.data)); - }) - .catch(function (error) { - alert('Failed to pause workflow, there could be a connection problem'); - console.log(error); - }); -} - -// Need to think about making this async -function resume_workflow(wf_id) { - let config = _build_config('patch', _resource(wf_id), {option: 'resume'}); - - return axios(config) - .then(function (response) { - console.log(JSON.stringify(response.data)); - }) - .catch(function (error) { - alert('Failed to resume workflow, there could be a connection problem'); - console.log(error); - }); -} - -async function download_archive(wf_id) { - const url = _url(wf_id); - const path = Path.resolve(__dirname, wf_id + '.tgz') - const writer = fs.createWriteStream(path) - - const response = await axios({ - url, - method: 'patch', - responseType: 'stream', - data: { wf_id }, - proxy: false, - }); - response.data.pipe(writer); - return new Promise((resolve, reject) => { - writer.on('finish', resolve); - writer.on('error', reject); - }); -} - -module.exports = { submit_workflow, query_workflow, start_workflow, - pause_workflow, resume_workflow, cancel_workflow, - reexecute_workflow, download_archive } diff --git a/beeflow/enhanced_client/renderer/config.js b/beeflow/enhanced_client/renderer/config.js deleted file mode 100644 index b7ed4fea8..000000000 --- a/beeflow/enhanced_client/renderer/config.js +++ /dev/null @@ -1,42 +0,0 @@ -const db = require('./database.js'); -const tunnel = require('./tunnel.js'); -let config = null; - -function init(hostname, moniker, bolt_port, wfm_sock) { - config = new Config(hostname, moniker, bolt_port, wfm_sock); - db.add_config(hostname, moniker, bolt_port, wfm_sock); - let tun = new tunnel.Tunnel(hostname, moniker, [ - { - local_port: 9999, - remote_socket: wfm_sock, - }, - { - local_port: 9995, - remote_port: bolt_port, - }, - ]); - tun.start(); -} - -function getWFMTunnel() { - return config.wfm_tunnel_port; -} - -function configLoaded() { - if (config !== null) { - return true; - } else { - return false; - } -} - -class Config { - constructor(hostname, moniker, bolt_port, wfm_sock) { - this.hostname = hostname; - this.moniker = moniker; - this.bolt_port = bolt_port; - this.wfm_sock = wfm_sock; - } -} - -module.exports = { init } diff --git a/beeflow/enhanced_client/renderer/control.js b/beeflow/enhanced_client/renderer/control.js deleted file mode 100644 index a4bc9aaa1..000000000 --- a/beeflow/enhanced_client/renderer/control.js +++ /dev/null @@ -1,67 +0,0 @@ -const viz = require('./viz.js'); -const tunnel = require('./tunnel.js'); - -// Set up control handlers for the page -function setup(opts) { - let hostname = document.getElementById(opts.hostname); - let hostnameError = document.getElementById(opts.hostnameError); - let moniker = document.getElementById(opts.moniker); - let monikerError = document.getElementById(opts.monikerError); - let boltPort = document.getElementById(opts.boltPort); - let boltPortError = document.getElementById(opts.boltPortError); - let submitButton = document.getElementById(opts.submitButton); - let reloadButton = document.getElementById(opts.reloadButton); - - function draw() { - viz.draw(opts.vizContainer, boltPort.value) - .catch(err => { - opts.showErrorMessage('An error occurred while establishing a connection. Please check your configuration.'); - console.log('Connection/Drawing error:'); - console.log(err); - }); - } - - let validateFields = [ - [hostname, hostnameError, "Hostname"], - [moniker, monikerError, "Moniker"], - [boltPort, boltPortError, "Bolt Port"], - ]; - submitButton.addEventListener('click', ev => { - // Reset all input error messages - hostnameError.innerText = ""; - monikerError.innerText = ""; - boltPortError.innerText = ""; - // Check for empty inputs - let ok = true; - for (let [field, error, name] of validateFields) { - if (field.value.trim().length == 0) { - error.innerText = `* ${name} cannot be empty`; - ok = false; - } - } - - // An error occurred - if (!ok) { - return; - } - - // Set up the tunnel and draw - tunnel.connect({ - hostname: hostname.value, - moniker: moniker.value, - port: boltPort.value, - }); - // Wait 10 seconds for the tunnel to set up - let message = opts.showMessage('Connecting...'); - setTimeout(() => { - message.remove(); - draw(); - }, 10000); - }); - - reloadButton.addEventListener('click', ev => { - draw(); - }); -} - -module.exports = { setup }; diff --git a/beeflow/enhanced_client/renderer/database.js b/beeflow/enhanced_client/renderer/database.js deleted file mode 100644 index 73eb17b83..000000000 --- a/beeflow/enhanced_client/renderer/database.js +++ /dev/null @@ -1,162 +0,0 @@ -// Database code using the window.localStorage object. - -const DB_NAME = 'BeeClient'; -const WORKFLOWS = 'workflows'; -const CLUSTERS = 'clusters'; - -let store = window.localStorage; - -// *_key() functions are used to determine the key within the localStorage -// object. -// -// Database objects are separated by using different key prefixes. For example, -// a key prefixed with 'workflows:' is used for a workflow object. -// - -function workflow_key(wf_id) { - return `workflows:${wf_id}`; -} - -function is_workflow_key(key) { - return key.startsWith('workflows:'); -} - -function task_key(wf_id, task_id) { - return `tasks:${wf_id}:${task_id}`; -} - -// Return true if this is a task for the given workflow -function is_workflow_task_key(key, wf_id) { - return key.startsWith(`tasks:${wf_id}`); -} - -function cluster_key(cluster_id) { - return `clusters:${cluster_id}`; -} - -function is_cluster_key(key) { - return key.startsWith('clusters:'); -} - -function encode(obj) { - return JSON.stringify(obj); -} - -function decode(s) { - return JSON.parse(s); -} - -function init() { - // TODO: Remove this? -} - -// Helper function to make it easier to iterate over elements of the store -function for_each_element(check, body) { - for (let i = 0; i < store.length; i++) { - let key = store.key(i); - if (check(key)) { - body(key, store.getItem(key)); - } - } -} - -// Add a WF -function add_wf(wf_id, name) { - let wf = { - wf_id, - completed: 'False', - archived: 'False', - percentage_complete: 0, - status: 'Pending', - name, - }; - store.setItem(workflow_key(wf_id), encode(wf)); -} - -// Add a cluster configuration -function add_config(hostname, moniker, bolt_port, wfm_sock) { - let id = store.getItem('next_cluster_id'); - if (id === null) { - id = 0; - } - let config = { - hostname, - moniker, - bolt_port, - wfm_sock, - }; - store.setItem(cluster_key(id), encode(config)); - // Increment the next id - store.setItem('next_cluster_id', id + 1); - return id; -} - -// Get all saved cluster configs -function get_cluster_configs() { - let clusters = []; - for_each_element(key => is_cluster_key(key), (key, cluster) => { - clusters.push(decode(cluster)); - }); - return clusters; -} - -// Get a parituclar wf -function get_wf(wf_id) { - return decode(store.getItem(workflow_key(wf_id))); -} - -// Get all workflows in the system -function get_workflows() { - let workflows = []; - for_each_element(key => is_workflow_key(key), (key, workflow) => { - workflows.push(decode(workflow)); - }); - return workflows; -} - -// Get all tasks associated with a wf_id -function get_tasks(wf_id) { - let tasks = []; - for_each_element(key => is_workflow_task_key(key, wf_id), (key, task) => { - tasks.push(decode(task)); - }); - return tasks; -} - -function update_task_state(task_id, wf_id, status) { - let key = task_key(wf_id, task_id); - let task = decode(store.getItem(key)); - task.status = status; - store.setItem(key, encode(task)); -} - -function delete_wf(wf_id) { - // Note: this doesn't delete the tasks - store.removeItem(workflow_key(wf_id)); -} - -function add_task(task_id, wf_id, name, resource, base_command, status) { - let key = task_key(wf_id, task_id); - let task = { - wf_id, - task_id, - completed, - resource, - base_command, - status, - }; - store.setItem(key, encode(task)); -} - -function delete_task(wf_id, task_id) { - store.removeItem(task_key(wf_id, task_id)); -} - -// Delete everything -function clear() { - store.clear(); -} - -module.exports = { init, add_wf, get_wf, get_workflows, get_tasks, delete_wf, - add_config, get_cluster_configs, add_task, delete_task, - clear }; diff --git a/beeflow/enhanced_client/renderer/display.js b/beeflow/enhanced_client/renderer/display.js deleted file mode 100644 index 24f0069cc..000000000 --- a/beeflow/enhanced_client/renderer/display.js +++ /dev/null @@ -1,364 +0,0 @@ -/* - * This file comtains several objects for components in our app - * - * - * */ - -components = new Map(); -buttons = new Map(); -// The current content displayed in the main window -currentContent = null; - -const wf = require('./workflows.js'); -const config = require('./config.js'); -const db = require('./database.js'); - -// Add extra buttons unrelated to a component -// Setup start button -function startButton(button_id) { - button = document.getElementById(button_id); - // Create a click method listener for the button - button.addEventListener('click', e => { - console.log('Clicked start'); - wf.start_workflow(); - document.getElementById('start-wf_button').style.display = "none"; - document.getElementById('pause-wf_button').style.display = "inline"; - }); -} - -// Setup pause button -function downloadButton(button_id) { - button = document.getElementById(button_id); - // Create a click method listener for the button - button.addEventListener('click', e => { - console.log('Clicked download'); - // Breaks seperations of concerns add to button map and lookup - console.log('Downloading') - wf.download_current_archive(); - }); -} - -// Setup pause button -function pauseButton(button_id) { - button = document.getElementById(button_id); - // Create a click method listener for the button - button.addEventListener('click', e => { - console.log('Clicked pause'); - // Breaks seperations of concerns add to button map and lookup - wf.pause_workflow(); - document.getElementById('pause-wf_button').style.display = "none"; - document.getElementById('resume-wf_button').style.display = "inline"; - }); -} - -// Add extra buttons unrelated to a component -// Setup start button -function resumeButton(button_id) { - button = document.getElementById(button_id); - // Create a click method listener for the button - button.addEventListener('click', e => { - wf.resume_workflow(); - document.getElementById('resume-wf_button').style.display = "none"; - document.getElementById('pause-wf_button').style.display = "inline"; - }); -} - -function updateButton(button_id) { - button = document.getElementById(button_id); - // Create a click method listener for the button - button.addEventListener('click', e => { - wf.update_current_workflow(); - }); -} - -class Component { - constructor(content_id, button_id, form_button_id) { - this.content_id = content_id; - this.element = document.getElementById(content_id); - // Add to components map - components.set(content_id, this.element); - // Setup our button if we have one - if (button_id !== null) { - this.button_id = button_id; - this.button = document.getElementById(this.button_id); - // Add button to buttons map keyed on it's ID - buttons.set(this.button_id, this.button); - // Setup an event listener for when the button is clicked - this.setupButtonListener(); - } - // Setup form if we have one - if (form_button_id !== null) { - this.form_button_id = form_button_id; - // Get for button element then attach a listener to it - this.form = document.getElementById(this.form_button_id); - this.setupFormListener(); - } - } - - // Event listener for a form if the component has one - // Every component except welcomeMessage has one - // This is an abstract method - setupFormListener() { - throw new Error("Form listener needs to be implemented in child class"); - } - - // Do something when the particular component is toggled - onToggle() {} - - // Listener for the left menu button. Toggles the main content with the - // specific menu and sets its button to active. - setupButtonListener() { - // Create a click method listener for the button - if (this.button) { - this.button.addEventListener('click', e => { - // Toggle the component on or off and toggle the associated button - this.toggle_content(); - // this.toggle_button(add_wf_button, main_button_set) - this.toggle_button(); - }) - } - } - - // Toggle the component on or off - toggle_content() { - if (this.element.style.display === 'inline'){ - this.element.style.display = 'none'; - // Return to main window - currentContent.style.display = 'inline'; - } else { - let temp_components = new Map(components); - temp_components.delete(this.component_id); - for (let component of components.values()) { - component.style.display = 'none'; - } - this.element.style.display = 'inline'; - currentContent.style.display = 'none'; - // Let the element do an update, if needed - this.onToggle(); - } - } - - // This highlights the button of the associated component when it is active - toggle_button() { - if (this.button.classList.contains('is-active')) { - this.button.classList.remove("is-active"); - } else { - // Create a button map and remove the current button from it - let temp_buttons = new Map(buttons); - temp_buttons.delete(this.button_id); - // Iterate through the button objects - for (let button of temp_buttons.values()) { - if (button.classList.contains("is-active")) { - button.classList.remove("is-active"); - } - } - this.button.classList.add("is-active"); - } - } -} - -class AddWorkflow extends Component { - constructor(content_id, button_id, form_button_id) { - super(content_id, button_id, form_button_id); - } - - setupFormListener() { - this.form.addEventListener('click', async e => { - // Disable the button during submission - this.form.disabled = true; - // Need to add checking for valid values - // Get all the form contents then pass to add workflow function - let name = document.getElementById('add-wf_name').value; - let main_cwl = document.getElementById('add-wf_cwl').value; - let yaml = document.getElementById('add-wf_yaml').value; - let workdir = document.getElementById('add-wf_workdir').value; - console.log(document.getElementById('add-wf_tar')); - let file = document.getElementById('add-wf_tar').files[0]; - let tarball_path = file.path; - let tarball_fname = file.name; - wf.add_workflow(name, main_cwl, yaml, workdir, tarball_path, tarball_fname) - .then(wf_id => { - // TODO: Do something with the WF ID. - // Reset the form - document.getElementById('add-workflow_form').reset(); - document.getElementById('start-wf_button').style.display = "inline"; - document.getElementById('pause-wf_button').style.display = "none"; - document.getElementById('resume-wf_button').style.display = "none"; - hideWelcome(); - this.toggle_content(); - this.toggle_button(); - // Re-enable the button - this.disabled = false; - }) - .catch(err => { - alert("An error occurred while adding a workflow"); - }) - }); - } -} - -class Settings extends Component { - constructor(content_id, button_id, form_button_id) { - super(content_id, button_id, form_button_id); - } - - setupFormListener() { - this.form.addEventListener('click', e => { - let hostname = document.getElementById('settings-hostname').value; - let moniker = document.getElementById('settings-moniker').value; - let bolt_port = document.getElementById('settings-bolt_port').value; - let wfm_sock = document.getElementById('settings-wfm_socket').value; - config.init(hostname, moniker, bolt_port, wfm_sock); - this.toggle_content(); - this.toggle_button(); - }) - } -} - -class DeleteWorkflow extends Component { - constructor(content_id, button_id, form_button_id) { - super(content_id, button_id, form_button_id); - } - - setupFormListener() { - this.form.addEventListener('click', e => { - let wf_id = document.getElementById('delete-wf_id').value; - wf.delete_workflow(wf_id); - showWelcome(); - document.getElementById('delete-workflow_form').reset(); - this.toggle_content(); - this.toggle_button(); - document.getElementById('start-wf_button').style.display = "inline"; - document.getElementById('pause-wf_button').style.display = "none"; - document.getElementById('resume-wf_button').style.display = "none"; - }); - } -} - -class ReexecuteWorkflow extends Component { - constructor(content_id, button_id, form_button_id) { - super(content_id, button_id, form_button_id); - } - - setupFormListener() { - // wf.add_workflow() - this.form.addEventListener('click', async e => { - // Get all the form contents then pass to add workflow function - let name = document.getElementById('reexecute-wf_name').value; - let tarball_path = document.getElementById('reexecute-wf_tar').files[0].path; - wf.reexecute_workflow(name, tarball_path) - document.getElementById('reexecute-workflow_form').reset(); - hideWelcome(); - document.getElementById('start-wf_button').style.display = "inline"; - document.getElementById('pause-wf_button').style.display = "none"; - document.getElementById('resume-wf_button').style.display = "none"; - this.toggle_content(); - this.toggle_button(); - }) - } -} - -class SettingsList extends Component { - constructor(content_id, button_id, form_button_id) { - super(content_id, button_id, form_button_id); - let clearButton = document.querySelector('#clearButton'); - clearButton.addEventListener('click', () => { - if (confirm('Are you sure you want to do this? This will delete everything.')) { - db.clear(); - this.doUpdate(); - } - }); - } - - doUpdate() { - // TODO: Fill other settings info - // Display the current list of cluster configs - let list = document.createElement('ul'); - for (let cluster of db.get_cluster_configs()) { - let item = document.createElement('li'); - item.innerText = `${cluster.moniker}@${cluster.hostname}`; - list.appendChild(item); - } - let configs = document.querySelector('#clusterConfigs'); - configs.replaceChildren(list); - } - - onToggle() { - this.doUpdate(); - } -} - -class CurrentWorkflow extends Component { - constructor(content_id, button_id, form_button_id) { - super(content_id, button_id, form_button_id); - // TODO - } - - onToggle() { - // TODO: Fill the settings based on current workflow ID - } -} - -function initContent() { - currentContent = components.get("welcomeMessage"); -} - -// Component factory -function addComponent(content_id, button_id = null, form_button_id = null) { - switch(content_id) { - case 'addWorkflow': - component = new AddWorkflow(content_id, button_id, form_button_id); - break; - case 'deleteWorkflow': - component = new DeleteWorkflow(content_id, button_id, form_button_id); - break; - case 'reexecuteWorkflow': - component = new ReexecuteWorkflow(content_id, button_id, form_button_id); - break; - case 'settings': - component = new Settings(content_id, button_id, form_button_id); - break; - case 'settingsList': - component = new SettingsList(content_id, button_id, form_button_id); - break; - case 'currentWorkflow': - component = new CurrentWorkflow(content_id, button_id, form_button_id); - break; - default: - // welcomeMessage and currentWorkflow just use Component - component = new Component(content_id, button_id, form_button_id); - } -} - -function hideWelcome() { - document.getElementById('welcomeMessage').style.display = "none"; -} - -function showWelcome() { - document.getElementById('welcomeMessage').style.display = "inline"; -} - -// Initialize the workflow list -function initWorkflows(container_id) { - // Dummy workflows - let workflows = [ - { - name: 'clamr', - }, - { - name: 'cat-grep-tar', - }, - ]; - let list = document.createElement('ul'); - for (let workflow of workflows) { - let item = document.createElement('li'); - item.innerText = workflow.name; - list.appendChild(item); - } - let container = document.getElementById(container_id); - container.replaceChildren(list); - // TODO -} - -module.exports = { Component, addComponent, startButton, downloadButton, pauseButton, hideWelcome, - resumeButton, updateButton, initContent, hideWelcome, showWelcome, initWorkflows } diff --git a/beeflow/enhanced_client/renderer/gdb.js b/beeflow/enhanced_client/renderer/gdb.js deleted file mode 100644 index 33eb3de27..000000000 --- a/beeflow/enhanced_client/renderer/gdb.js +++ /dev/null @@ -1,21 +0,0 @@ -const neo4j = require('neo4j-driver'); - -function run() { - const uri = 'bolt://127.0.0.1:34273'; - const driver = neo4j.driver(uri, neo4j.auth.basic('neo4j', 'password')); - const session = driver.session(); - - session.run('MATCH (n) RETURN n') - .then(result => { - console.log(result); - }) - .catch(err => { - console.log(err); - }) - .finally(() => { - session.close(); - driver.close(); - }); -} - -module.exports = { run }; diff --git a/beeflow/enhanced_client/renderer/img/logo.png b/beeflow/enhanced_client/renderer/img/logo.png deleted file mode 100644 index 5d5b48d8e..000000000 Binary files a/beeflow/enhanced_client/renderer/img/logo.png and /dev/null differ diff --git a/beeflow/enhanced_client/renderer/main.html b/beeflow/enhanced_client/renderer/main.html deleted file mode 100644 index 364c6d9dc..000000000 --- a/beeflow/enhanced_client/renderer/main.html +++ /dev/null @@ -1,74 +0,0 @@ - - - - - BEE Viz - - - - - -
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a/beeflow/enhanced_client/renderer/styles/main.css +++ /dev/null @@ -1,24 +0,0 @@ -#title { - display: inline; -} -/* Logo right next to the header */ -#logo { - vertical-align: middle; - display: inline-block; - width: 80px; - height: 80px; - background: url('../img/logo.png'); - background-size: contain; - background-repeat: no-repeat; -} - -#sidebar { - max-width: 400px; - margin: 1em; -} - -#viz { - border: 2px solid black; - margin: 1em; - height: 700px; -} diff --git a/beeflow/enhanced_client/renderer/tunnel.js b/beeflow/enhanced_client/renderer/tunnel.js deleted file mode 100644 index 0547fe47e..000000000 --- a/beeflow/enhanced_client/renderer/tunnel.js +++ /dev/null @@ -1,25 +0,0 @@ -const { spawn } = require('child_process'); -const fs = require('fs') - -// Spawn an SSH tunnel connection -function connect(opts) { - let out = fs.openSync('./out.log', 'a'); - let args = [ - '-fN', - '-L', - `${opts.port}:localhost:${opts.port}`, - `${opts.moniker}@${opts.hostname}`, - ]; - - const tunnel = spawn('ssh', args, { - stdio: ['ignore', out, out], - shell: false, - detach: true, - }); - - process.on('exit', () => { - tunnel.kill(); - }); -} - -module.exports = { connect }; diff --git a/beeflow/enhanced_client/renderer/viz.html b/beeflow/enhanced_client/renderer/viz.html deleted file mode 100644 index 472ebce2c..000000000 --- a/beeflow/enhanced_client/renderer/viz.html +++ /dev/null @@ -1,17 +0,0 @@ - - - DataViz - - - - - -
-
- - diff --git a/beeflow/enhanced_client/renderer/viz.js b/beeflow/enhanced_client/renderer/viz.js deleted file mode 100644 index 110aaacf0..000000000 --- a/beeflow/enhanced_client/renderer/viz.js +++ /dev/null @@ -1,54 +0,0 @@ -// const {NeoVis} = require('neovis.js'); - -let initialized = false; - -function draw(containerId, boltPort) { - var config = { - containerId, - neo4j: { - serverUrl: `bolt://127.0.0.1:${boltPort}`, - serverUser: "neo4j", - serverPassword: "password", - }, - } - var cypher = { - labels: { - "Task": { - label: "name" - }, - "Metadata": { - label: "state" - }, - }, - relationships: { - "DEPENDS_ON": { - caption: true, - }, - "DESCRIBES": { - caption: false - }, - }, - hierarchical: true, - hierarchical_sort_method: "directed", - randomSeed: 0, - initialCypher: "MATCH p=()-[r:DEPENDS_ON|:DESCRIBES]->() RETURN p", - }; - - var final = { - ...config, - ...cypher - }; - var viz = new NeoVis.default(final); - // Create a wrapper promise for handling errors - let p = new Promise((resolve, reject) => { - viz.registerOnEvent('error', err => { - reject(err); - }); - }); - // Start rendering - viz.render(); - initialized = true; - return p; -} - -module.exports = { draw }; diff --git a/beeflow/enhanced_client/renderer/workflows.js b/beeflow/enhanced_client/renderer/workflows.js deleted file mode 100644 index cdcdead85..000000000 --- a/beeflow/enhanced_client/renderer/workflows.js +++ /dev/null @@ -1,249 +0,0 @@ -/* - * This file contains code that manages workflows in the app - * - * - */ - -const client = require('./client.js'); -const db = require('./database.js'); -const display = require('./display.js'); -const config = require('./config.js'); -const viz = require('./viz.js'); -//const workflows = new Map(); -var workflow_list = null; - -currentWorkflow = null - -// Load workflows from database and initialize workflowList -function initialize(wf_list_id) { - // Load all the workflows from the database - // workflows = db.get_workflows(); - // console.log('Workflows'); - // console.log(workflows); - // // Setup workflow list and populate it with stuff from database - workflow_list = new WorkflowList(wf_list_id); - // for (workflow in workflows) { - // workflow_list.add(workflow); - // } -} - -class Workflow { - // Constructor for workflow object - constructor(name, main_cwl, yaml, workdir, tarball_path, tarball_fname) { - this.name = name; - this.main_cwl = main_cwl; - this.yaml = yaml; - this.workdir = workdir; - this.tarball_path = tarball_path; - this.tarball_fname = tarball_fname; - this.id = 'Pending'; - this.status = 'Pending'; - } -} - -class WorkflowList { - constructor(wf_list_id) { - this.list = document.getElementById(wf_list_id); - //console.log(this.list); - } - - add(workflow) { - var newItem = document.createElement('li'); - newItem.innerHTML = "" + workflow.name + ""; - newItem.className = "is-size-1"; - newItem.id = workflow.id; - newItem.addEventListener('click', function () { - // Set the main content area to show this workflow - }); - this.list.appendChild(newItem); - } - - delete(wf_id) { - var elements = this.list.getElementsByTagName("li"); - var len = elements.length; - - for (var i = 0; i < len; i++) { - if (elements[i].id == wf_id) { - this.list.removeChild(elements[i]); - break; - } - } - } -} - -// Add a new workflow -async function add_workflow(name, main_cwl, yaml, workdir, tarball_path, tarball_fname) { - // Submit workflow to workflow manager - // Create new WF object - let new_workflow = new Workflow(name, main_cwl, yaml, workdir, tarball_path, tarball_fname); - let {wf_id, tasks} = await client.submit_workflow(new_workflow); - - new_workflow.id = wf_id; - //workflows.add(wf_id, new_workflow); - // Add wf to the navigation list - workflow_list.add(new_workflow); - // Add to the database - db.add_wf(wf_id, name); - for (task_id in tasks) { - let name = tasks[task_id]['name']; - let base_command = tasks[task_id]['command']; - let task_status = tasks[task_id]['status']; - db.add_task(task_id, wf_id, name, config.resource, base_command, task_status); - } - - // Make this workflow appear in the main workflow section - set_current_workflow(new_workflow); - // Remove the welcome message if currently displayed - if (currentContent === welcomeMessage) { - currentContent = currentWorkflow; - } - - return wf_id; -} - -function start_workflow() { - wf_id = currentWorkflow.id; - client.start_workflow(wf_id); -} - -function delete_workflow(wf_id) { - db.delete_wf(wf_id); - client.cancel_workflow(wf_id); - workflow_list.delete(wf_id); - remove_current_workflow(wf_id); -} - -function copy_workflow(wf_id, path) { - client.copy(wf_id, path); -} - -function reexecute_workflow(name, tarball_path) { - (async () => { - // Create new WF object - let new_workflow = new Workflow(name, "", "", tarball_path); - let {wf_id, tasks} = await client.reexecute_workflow(new_workflow); - - new_workflow.id = wf_id; - //workflows.add(wf_id, new_workflow); - // Add wf to the navigation list - workflow_list.add(new_workflow); - // Add to the database - db.add_wf(wf_id, name); - for (task_id in tasks) { - let name = tasks[task_id]['name']; - let base_command = tasks[task_id]['command']; - let task_status = tasks[task_id]['status']; - db.add_task(task_id, wf_id, name, config.resource, base_command, task_status); - } - - // Make this workflow appear in the main workflow section - set_current_workflow(new_workflow); - // Remove the welcome message if currently displayed - if (currentContent === welcomeMessage) { - currentContent = currentWorkflow; - } - })(); -} - -function pause_workflow(wf_id) { - client.pause_workflow(wf_id); -} - -function resume_workflow(wf_id) { - client.resume_workflow(wf_id); -} - -function have_workflows() { - return workflows.size > 0; -} - -function remove_current_workflow(workflow) { - // We have more workflows set to first one - if (workflows.size > 0) { - const new_workflow = [...workflows][0]; - set_current_workflow(workflow); - } -} - -function create_task_list(tasks) { - for (task_id in tasks) { - let name = tasks[task_id]['name']; - let base_command = tasks[task_id]['command']; - let task_status = tasks[task_id]['status']; - var newTask = document.createElement('li'); - newTask.innerHTML = "

" + name + " " + task_status + "

"; - taskList.appendChild(newTask); - } -} - -// Set the current workflow -function set_current_workflow(workflow) { - (async () => { - currentWorkflow = workflow; - let current_wf_status = document.getElementById('current-wf_status'); - let current_wf_resource = document.getElementById('current-wf_resource'); - let current_wf_name = document.getElementById('current-wf_name'); - let current_wf_id = document.getElementById('current-wf_id'); - - // Modify the variables used for the current workflow - current_wf_status.innerHTML = workflow.status; - current_wf_resource.innerHTML = 'fg-rfe1'; - current_wf_name.innerHTML = workflow.name; - current_wf_id.innerHTML = workflow.id; - - // Need to add some additional logic here and make this truly asynchronous - let {wf_status, tasks} = await client.query_workflow(workflow.id); - - // Set visualiation - document.getElementById('viz').src = "viz.html"; - current_wf_status.innerHTML = wf_status; - taskList = document.getElementById('taskList'); - taskList.innerHTML = ''; - - for (task_id in tasks) { - let name = tasks[task_id]['name']; - let base_command = tasks[task_id]['command']; - let task_status = tasks[task_id]['status']; - var newTask = document.createElement('li'); - newTask.innerHTML = "

" + name + " " + task_status + "

"; - taskList.appendChild(newTask); - } - })(); -} - -function download_current_archive() { - wf_id = currentWorkflow.id; - client.download_archive(wf_id); - console.log(wf_id) -} - -function update_current_workflow() { - (async () => { - // Query status of tasks - wf_id = currentWorkflow.id; - let {wf_status, tasks} = await client.query_workflow(wf_id); - - // Update visualization - document.getElementById('viz').contentWindow.location.reload(); - let current_wf_status = document.getElementById('current-wf_status'); - current_wf_status.innerHTML = wf_status; - - taskList = document.getElementById('taskList'); - taskList.innerHTML = ''; - - for (task_id in tasks) { - let name = tasks[task_id]['name'] - let base_command = tasks[task_id]['command'] - let task_status = tasks[task_id]['status'] - var newTask = document.createElement('li'); - newTask.innerHTML = "

" + name + " " + task_status + "

"; - taskList.appendChild(newTask) - } - })(); -} - -// Set the things we want to export -module.exports = { initialize, workflows, add_workflow, start_workflow, - update_current_workflow, Workflow, have_workflows, - pause_workflow, resume_workflow, delete_workflow, workflows, - download_current_archive, reexecute_workflow } diff --git a/beeflow/remote/remote.py b/beeflow/remote/remote.py new file mode 100644 index 000000000..70cc6cf09 --- /dev/null +++ b/beeflow/remote/remote.py @@ -0,0 +1,161 @@ +"""This script manages an API that allows the remote submission of jobs.""" +import os +import socket +import pathlib +from fastapi import FastAPI +import uvicorn + +from beeflow.common import cli_connection +from beeflow.common import paths +from beeflow.client import bee_client +from beeflow.common.config_driver import BeeConfig as bc + + +app = FastAPI() + + +@app.get("/") +def read_root(): + """Get REST Connection info.""" + return {"Endpoint info": "BEEflow core API: Documentation - https://lanl.github.io/BEE/"} + + +@app.get("/workflows/status/") +def get_wf_status(): + """WIP - This endpoint is planned to give you a status on an actively running workflow.""" + + +@app.get("/droppoint") +def get_drop_point(): + """Transmit the scp location to be used for the storage of workflow tarballs. + + Users are required to ensure that this directory has the appropriate permissions. + """ + output = {} + output["droppoint"] = str(paths.droppoint_root()) + return output + + +@app.get("/owner") +def get_owner(): + """Transmit the owner of this BEEflow instance.""" + user_name = os.getenv('USER') or os.getenv('USERNAME') + return user_name + + +@app.get("/submit/{filename}") +def submit_new_wf(filename: str): + """WIP: Submit a new workflow with a tarball for the workflow at a given path.""" + return filename + + +@app.get("/submit_long/{wf_name}/{tarball_name}/{main_cwl_file}/{job_file}") +def submit_new_wf_long(wf_name: str, tarball_name: str, main_cwl_file: str, job_file: str): + r"""Submit a new workflow with a tarball for the workflow at a given path. + + This makes the following assumptions:\n + The workflow tarball should be at /\n + The workdir should be at /-workdir and + should have the required input files. + """ + output = {} + # Append the droppoint path to the tarball_name + workflow_path = paths.droppoint_root() + "/" + tarball_name + # Make a workdir path + workdir_path = paths.droppoint_root() + "/" + tarball_name.replace(".tgz", "") + "-workdir" + # Make sure that the directory exists, if not create it with owner-only permissions + if not os.path.exists(workdir_path): + os.makedirs(workdir_path, mode=0o700) + + # Validate the path to the tarball. + if not os.path.exists(workflow_path): + output["error"] = "The workflow tarball name provided was not found in the drop point." + return output + + # Convert the paths to pathlib paths. + workflow_path = pathlib.Path(workflow_path) + workdir_path = pathlib.Path(workdir_path) + + try: + bee_client.submit(wf_name, + workflow_path, + main_cwl_file, + job_file, + workdir_path, + no_start=False) + output["result"] = "Submitted new workflow" + str(wf_name) + return output + except bee_client.ClientError as error: + output["error"] = str(error) + return output + + +@app.get("/showdrops") +def show_drops(): + """WIP: This endpoint will give a list of workflows in the droppoint.""" + + +@app.get("/cleanup") +def cleanup_wf_directory(): + """WIP: This endpoint is planned to delete all the temporarily stored workflow tarballs.""" + + +@app.get("/core/status/") +def get_core_status(): + """Check the status of BEEflow and the components.""" + output = {} + resp = cli_connection.send(paths.beeflow_socket(), {'type': 'status'}) + if resp is None: + output["error"] = 'Cannot connect to the beeflow daemon, is it running?' + return output + for comp, stat in resp['components'].items(): + output[comp] = stat + return output + + +def is_port_taken(port, host='127.0.0.1'): + """Check if a port is in use on the given host.""" + with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: + try: + s.bind((host, port)) + except socket.error: + return True # Port is taken + return False # Port is free + + +def find_free_port(start_port=1024, end_port=65535, host='127.0.0.1'): + """Search for a free port within the given range.""" + for port in range(start_port, end_port): + with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: + try: + s.bind((host, port)) + return port # Return the first free port found + except socket.error: + continue # If the port is in use, try the next one + raise RuntimeError(f"No free port found in range {start_port}-{end_port}") + + +def create_app(): + """Start the web-server for the API with uvicorn.""" + # decide what port we're using for the long term. I set it to port 7777 temporarily + + port_number = bc.get('DEFAULT', 'remote_api_port') + if is_port_taken(port_number) is True: + print("Requested port number is unavailable, attempting to map port dynamically") + + port_number = find_free_port() + print(f"Available port found: {port_number}") + + config = uvicorn.Config("beeflow.remote.remote:app", + host="0.0.0.0", + port=port_number, + reload=True, + log_level="info") + server = uvicorn.Server(config) + + try: + server.run() + except OSError as exception: + if exception.errno == 98: + print(f"Selected port {port_number} is already in use.") + raise diff --git a/beeflow/task_manager/background.py b/beeflow/task_manager/background.py index 2c1360fbd..58da80036 100644 --- a/beeflow/task_manager/background.py +++ b/beeflow/task_manager/background.py @@ -9,25 +9,13 @@ from beeflow.common import log as bee_logging from beeflow.common.build.utils import ContainerBuildError from beeflow.common.build_interfaces import build_main +from beeflow.common.worker import WorkerError log = bee_logging.setup(__name__) - -def update_task_state(workflow_id, task_id, job_state, **kwargs): - """Informs the workflow manager of the current state of a task.""" - data = {'wf_id': workflow_id, 'task_id': task_id, 'job_state': job_state} - if 'metadata' in kwargs: - kwargs['metadata'] = jsonpickle.encode(kwargs['metadata']) - - if 'task_info' in kwargs: - kwargs['task_info'] = jsonpickle.encode(kwargs['task_info']) - - data.update(kwargs) - conn = utils.wfm_conn() - resp = conn.put(utils.wfm_resource_url("update/"), json=data) - if resp.status_code != 200: - log.warning("WFM not responding when sending task update.") +# States are based on https://slurm.schedmd.com/squeue.html#SECTION_JOB-STATE-CODES +COMPLETED_STATES = {'UNKNOWN', 'COMPLETED', 'CANCELLED', 'FAILED', 'TIMEOUT', 'TIMELIMIT'} def resolve_environment(task): @@ -46,7 +34,7 @@ def submit_task(db, worker, task): resolve_environment(task) log.info(f'Environment preparation complete for task {task.name}') job_id, job_state = worker.submit_task(task) - log.info(f'Job Submitted {task.name}: job_id: {job_id} job_state: {job_state}') + log.info(f"Job Submitted '{task.name}' job_id: {job_id} job_state: {job_state}") # place job in queue to monitor db.job_queue.push(task=task, job_id=job_id, job_state=job_state) # update_task_metadata(task.id, task_metadata) @@ -66,20 +54,18 @@ def submit_task(db, worker, task): return job_state -def submit_jobs(): +def submit_jobs(db): """Submit all jobs currently in submit queue to the workload scheduler.""" - db = utils.connect_db() worker = utils.worker_interface() while db.submit_queue.count() >= 1: # Single value dictionary task = db.submit_queue.pop() job_state = submit_task(db, worker, task) - update_task_state(task.workflow_id, task.id, job_state) + db.update_queue.push(task.workflow_id, task.id, job_state) -def update_jobs(): +def update_jobs(db): """Check and update states of jobs in queue, remove completed jobs.""" - db = utils.connect_db() worker = utils.worker_interface() # Need to make a copy first job_q = list(db.job_queue) @@ -88,44 +74,68 @@ def update_jobs(): task = job.task job_id = job.job_id job_state = job.job_state - new_job_state = worker.query_task(job_id) + + if job_state in COMPLETED_STATES: + # Completed states don't change. Remove from the job queue and move to the next job. + db.job_queue.remove_by_id(id_) + continue + + try: + new_job_state = worker.query_task(job_id) + except WorkerError as err: + log.warning(f'Failed to query job {job_id}: {err}') + new_job_state = 'UNKNOWN' # If state changes update the WFM if job_state != new_job_state: db.job_queue.update_job_state(id_, new_job_state) + log.info(f"Job Updated '{task.name}' job_id: {job_id} job_state: {new_job_state}") if new_job_state in ('FAILED', 'TIMELIMIT', 'TIMEOUT'): # Harvest lastest checkpoint file. task_checkpoint = task.get_full_requirement('beeflow:CheckpointRequirement') - log.info(f'state: {new_job_state}') log.info(f'TIMELIMIT/TIMEOUT task_checkpoint: {task_checkpoint}') if task_checkpoint: try: checkpoint_file = utils.get_restart_file(task_checkpoint, task.workdir) task_info = {'checkpoint_file': checkpoint_file, 'restart': True} - update_task_state(task.workflow_id, task.id, new_job_state, - task_info=task_info) + db.update_queue.push(task.workflow_id, task.id, new_job_state, + task_info=task_info) except utils.CheckpointRestartError as err: log.error(f'Checkpoint restart failed for {task.name} ({task.id}): {err}') - update_task_state(task.workflow_id, task.id, 'FAILED') + db.update_queue.push(task.workflow_id, task.id, 'FAILED') else: - update_task_state(task.workflow_id, task.id, new_job_state) - # States are based on https://slurm.schedmd.com/squeue.html#SECTION_JOB-STATE-CODES + db.update_queue.push(task.workflow_id, task.id, new_job_state) elif new_job_state in ('BOOT_FAIL', 'NODE_FAIL', 'OUT_OF_MEMORY', 'PREEMPTED'): # Don't update wfm, just resubmit - log.info(f'Task {task.name} in state {new_job_state}') log.info(f'Resubmitting task {task.name}') db.job_queue.remove_by_id(id_) job_state = submit_task(db, worker, task) - update_task_state(task.workflow_id, task.id, job_state) + db.update_queue.push(task.workflow_id, task.id, job_state) else: - update_task_state(task.workflow_id, task.id, new_job_state) + db.update_queue.push(task.workflow_id, task.id, new_job_state) - if job_state in ('ZOMBIE', 'COMPLETED', 'CANCELLED', 'FAILED', 'TIMEOUT', 'TIMELIMIT'): + if job_state in COMPLETED_STATES: # Remove from the job queue. Our job is finished db.job_queue.remove_by_id(id_) def process_queues(): """Look for newly submitted jobs and update status of scheduled jobs.""" - submit_jobs() - update_jobs() + db = utils.connect_db() + + # Submit and update jobs + submit_jobs(db) + update_jobs(db) + + # Attempt to send a batch of task updates to the wfm, otherwise keep the + # updates for later + state_updates = jsonpickle.encode(db.update_queue.updates()) + conn = utils.wfm_conn() + resp = conn.put(utils.wfm_resource_url("update/"), json={'state_updates': state_updates}) + if resp.status_code == 200: + # The workflow manager received the updates, so clear the queue + db.update_queue.clear() + else: + log.info(resp.json()['error']) + # Something bad happened so keep the udpates until the next round + log.warning("WFM not responding when sending task updates.") diff --git a/beeflow/tests/cf.cwl b/beeflow/tests/cf.cwl index 144bfb31b..aa8b34116 100644 --- a/beeflow/tests/cf.cwl +++ b/beeflow/tests/cf.cwl @@ -4,7 +4,9 @@ class: Workflow cwlVersion: v1.0 inputs: - infile: File + infile: + type: File + default: 'infile' outputs: clamr_dir: diff --git a/beeflow/tests/mocks.py b/beeflow/tests/mocks.py index f0f15d4f1..1d7cada86 100644 --- a/beeflow/tests/mocks.py +++ b/beeflow/tests/mocks.py @@ -84,6 +84,9 @@ def finalize_workflow(self): """Finalize the workflow.""" self._loaded = False + def set_workflow_state(self, state): + """Fake set wf state.""" + def create_requirement(self, req_class, key, value): """Fake creating a requirement.""" @@ -103,11 +106,11 @@ def execute_workflow(self): pass # noqa -class MockGDBInterface: - """A mock GDB interface. +class MockGDBDriver: + """A mock GDB driver. TODO: This is very crude, and will likely break with more complicated GDB - interactions. + interactions. This driver mock doesn't support multiple workflows per driver. """ def __init__(self, **_kwargs): @@ -121,7 +124,10 @@ def __init__(self, **_kwargs): self.outputs = {} def connect(self, **kwargs): - """Initialize a graph database interface with a driver.""" + """Connect driver to database.""" + + def create_bee_node(self): + """Create BEE head node.""" def initialize_workflow(self, workflow): """Begin construction of a workflow in the graph database.""" @@ -136,22 +142,22 @@ def _is_ready(self, task_id): return all(self.task_states[task_dep_id] == 'COMPLETED' for task_dep_id in task_deps) - def execute_workflow(self): + def execute_workflow(self, workflow_id): #noqa not using parameter in mock """Begin execution of the loaded workflow.""" self.workflow_state = 'RUNNING' for task_id in self.task_states: if self._is_ready(task_id): self.task_states[task_id] = 'READY' - def pause_workflow(self): + def pause_workflow(self, workflow_id): #noqa not using parameter in mock """Pause execution of a running workflow.""" self.workflow_state = 'PAUSED' - def resume_workflow(self): + def resume_workflow(self, workflow_id): #noqa not using parameter in mock """Resume execution of a running workflow.""" self.workflow_state = 'RESUME' - def reset_workflow(self, new_id): + def reset_workflow(self, old_id, new_id): #noqa not using parameter in mock """Reset the execution state and ID of a workflow.""" self.workflow = deepcopy(self.workflow) self.workflow.id = new_id @@ -160,10 +166,10 @@ def reset_workflow(self, new_id): self.task_metadata[task_id] = {} self.task_states[task_id] = 'WAITING' - def load_task(self, task): + def load_task(self, task, task_state): """Load a task into a workflow in the graph database.""" self.tasks[task.id] = task - self.task_states[task.id] = 'WAITING' + self.task_states[task.id] = task_state self.task_metadata[task.id] = {} self.inputs[task.id] = {} self.outputs[task.id] = {} @@ -172,7 +178,7 @@ def load_task(self, task): for outp in task.outputs: self.outputs[task.id][outp.id] = outp - def initialize_ready_tasks(self): + def initialize_ready_tasks(self, workflow_id): #noqa not using parameter in mock """Set runnable tasks in a workflow to ready.""" for task_id in self.tasks: if self._is_ready(task_id) and self.task_states[task_id] == 'WAITING': @@ -180,7 +186,8 @@ def initialize_ready_tasks(self): def restart_task(self, _old_task, new_task): """Create a new task from a failed task checkpoint restart enabled.""" - self.load_task(new_task) + task_state = "WAITING" + self.load_task(new_task, task_state) def finalize_task(self, task): """Set a task's state to completed.""" @@ -190,27 +197,27 @@ def get_task_by_id(self, task_id): """Return a workflow Task given its ID.""" return self.tasks[task_id] - def get_workflow_description(self): + def get_workflow_description(self, workflow_id): #noqa not using parameter in mock """Return the workflow description from the graph database.""" return deepcopy(self.workflow) - def get_workflow_state(self): + def get_workflow_state(self, workflow_id): #noqa not using parameter in mock """Return workflow's current state.""" return self.workflow_state - def set_workflow_state(self, state): + def set_workflow_state(self, workflow_id, state): #noqa not using parameter in mock """Return workflow's current state.""" self.workflow_state = state - def get_workflow_tasks(self): + def get_workflow_tasks(self, workflow_id): #noqa not using parameter in mock """Return a workflow's tasks from the graph database.""" return list(self.tasks.values()) - def get_workflow_requirements_and_hints(self): + def get_workflow_requirements_and_hints(self, workflow_id): #noqa not using parameter in mock """Return a tuple containing a list of requirements and a list of hints.""" return (None, None) - def get_ready_tasks(self): + def get_ready_tasks(self, workflow_id): #noqa not using parameter in mock """Return the tasks in a workflow with state 'READY'.""" return [task for task_id, task in self.tasks.items() if self.task_states[task_id] == 'READY'] @@ -282,28 +289,10 @@ def evaluate_expression(self, task, id_, output): step_inp.position, step_inp.value_from) - def workflow_completed(self): + def workflow_completed(self, workflow_id): #noqa not using parameter in mock """Return true if all of a workflow's final tasks have completed, else false.""" return all(state == 'COMPLETED' for state in self.task_states.values()) - def initialized(self): - """Return true if the database connection has been initialized, else false.""" - return not self.empty() - - def empty(self): - """Return true if the graph database is empty, else false.""" - return self.workflow is None - - def cleanup(self): - """Clean up all data in the graph database.""" - self.workflow = None - self.workflow_state = None - self.tasks.clear() - self.task_states.clear() - self.task_metadata.clear() - self.inputs.clear() - self.outputs.clear() - def close(self): """Close the connection to the graph database.""" diff --git a/beeflow/tests/test_config_validator.py b/beeflow/tests/test_config_validator.py index 4a77fb8e3..32677d3c1 100644 --- a/beeflow/tests/test_config_validator.py +++ b/beeflow/tests/test_config_validator.py @@ -6,10 +6,10 @@ def test_empty(): """Test an empty config.""" validator = ConfigValidator(description='empty test case') - assert validator.validate({}) == {} # noqa - # It should not allow any extra keys - with pytest.raises(ValueError): - validator.validate({'key': {}}) + assert validator.validate({}) == {} # noqa (suggestion is wrong for this case) + # Invalid sections and options should just print a warning rather than fail + assert validator.validate({'bad_section': {}}) == {} # noqa (suggestion is wrong for this case) + assert validator.validate({'bad_section': {'bad_option'}}) == {} # noqa (suggestion is wrong for this case) def test_two(): @@ -25,11 +25,11 @@ def test_two(): assert validator.validate(conf) == valid_conf # Test missing sections and values - with pytest.raises(ValueError): + with pytest.raises(ConfigError): validator.validate({'section1': {'key0': 'abc'}}) - with pytest.raises(ValueError): + with pytest.raises(ConfigError): validator.validate({}) - with pytest.raises(ValueError): + with pytest.raises(ConfigError): validator.validate({'section2': {'key0': 'something'}}) @@ -41,7 +41,7 @@ def test_choices(): assert (validator.validate({'section0': {'choice-key': 'B'}}) == {'section0': {'choice-key': 'B'}}) # noqa - with pytest.raises(ValueError): + with pytest.raises(ConfigError): assert validator.validate({'section0': {'choice-key': 'E'}}) @@ -54,9 +54,9 @@ def test_depends_on(): validator.section('two', info='section two', depends_on=('one', 'key', 'A')) validator.option('two', 'some-key', info='some other config value dependent on [one] key == A') - with pytest.raises(ValueError): + with pytest.raises(ConfigError): assert validator.validate({'one': {'key': 'B'}, 'two': {}}) - with pytest.raises(ValueError): + with pytest.raises(ConfigError): validator.validate({'one': {'key': 'A'}}) assert (validator.validate({'one': {'key': 'A'}, 'two': {'some-key': '123'}}) == {'one': {'key': 'A'}, 'two': {'some-key': '123'}}) # noqa @@ -71,7 +71,7 @@ def test_depends_on_order(): validator.section('one', info='section one') validator.option('one', 'key', choices=('A', 'B'), info='choice-based option') - # Sections must be listed in dependency order, so if section two dependends + # Sections must be listed in dependency order, so if section two depends # on section one, then section one must be listed first, then section two sections = validator.sections assert sections[0][0] == 'one' @@ -130,13 +130,12 @@ def test_missing_section(): info='defining an option, but the section is not defined') -def test_option_attr(): - """Test adding attributes to a section option.""" - validator = ConfigValidator(description='option with attribute') +def test_option_default(): + """Test setting a default value for an option.""" + validator = ConfigValidator(description='default option validator') validator.section('abc', info='some section') - validator.option('abc', 'test', info='some option with attributes', attrs={'key': 1}) + validator.option('abc', 'test', info='some option with attributes', validator=int, default=1) - opt_name, option = validator.options('abc')[0] - assert opt_name == 'test' - assert option.attrs == {'key': 1} + assert validator.validate({}) == {'abc': {'test': 1}} + assert validator.validate({'abc': {'test': 3}}) == {'abc': {'test': 3}} diff --git a/beeflow/tests/test_db_tm.py b/beeflow/tests/test_db_tm.py index c18b2f012..467ca77f2 100644 --- a/beeflow/tests/test_db_tm.py +++ b/beeflow/tests/test_db_tm.py @@ -145,6 +145,44 @@ def test_job_queue_update_job_state(temp_db): assert job.task == {8, 9, 10} assert job.job_id == 888 assert job.job_state == 'COMPLETED' + + +def test_update_queue_empty(temp_db): + """Test an empty update queue.""" + db = temp_db + + assert db.update_queue.updates() == [] + + db.update_queue.clear() + + assert db.update_queue.updates() == [] + + +def test_update_queue_order(temp_db): + """Ensure that updates are returned in the correct order.""" + db = temp_db + + db.update_queue.push('wf-id', 'task-id', 'RUNNING') + db.update_queue.push('wf-id', 'task-id', 'COMPLETED') + db.update_queue.push('wf-id-2', 'task-id-2', 'RUNNING') + db.update_queue.push('wf-id-2', 'task-id-2', 'FAILED') + + updates = db.update_queue.updates() + assert updates[0].wf_id == 'wf-id' + assert updates[0].task_id == 'task-id' + assert updates[0].job_state == 'RUNNING' + assert updates[1].wf_id == 'wf-id' + assert updates[1].task_id == 'task-id' + assert updates[1].job_state == 'COMPLETED' + assert updates[2].wf_id == 'wf-id-2' + assert updates[2].task_id == 'task-id-2' + assert updates[2].job_state == 'RUNNING' + assert updates[3].wf_id == 'wf-id-2' + assert updates[3].task_id == 'task-id-2' + assert updates[3].job_state == 'FAILED' + + db.update_queue.clear() + assert db.update_queue.updates() == [] # Ignore W0621: PyLama complains about redefining 'temp_db' from the outer # scope. This is how pytest fixtures work. # pylama:ignore=W0621 diff --git a/beeflow/tests/test_parser.py b/beeflow/tests/test_parser.py index ed41b58f1..2ba641770 100644 --- a/beeflow/tests/test_parser.py +++ b/beeflow/tests/test_parser.py @@ -3,7 +3,7 @@ from pathlib import Path import unittest -from beeflow.common.parser import CwlParser +from beeflow.common.parser import CwlParser, CwlParseError from beeflow.common.wf_data import (generate_workflow_id, Workflow, Task, Hint, StepInput, StepOutput, InputParameter, OutputParameter) @@ -50,6 +50,30 @@ def test_parse_workflow_script(self): for task in tasks: self.assertEqual(task.workflow_id, workflow_id) + def test_parse_workflow_validate_script(self): + """Test parsing of workflow and validate pre/post script files.""" + cwl_wf_file = find("beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_wf.cwl") #noqa + cwl_job_yaml = find("beeflow/data/cwl/bee_workflows/clamr-ffmpeg-validate_script/clamr_job.yml") #noqa + + workflow_id = generate_workflow_id() + + with self.assertRaises(Exception) as context: + self.parser.parse_workflow(workflow_id, cwl_wf_file, cwl_job_yaml) + + self.assertEqual(context.exception.args[0], "No shebang line found in pre_run.sh") + + def test_parse_workflow_validate_shell(self): + """Test parsing of workflow and check shell option matches pre/post script shebang line.""" + cwl_wf_file = find("ci/test_workflows/shell_validate/workflow.cwl") #noqa + cwl_job_yaml = find("ci/test_workflows/shell_validate/input.yml") #noqa + + workflow_id = generate_workflow_id() + + with self.assertRaises(Exception) as context: + self.parser.parse_workflow(workflow_id, cwl_wf_file, cwl_job_yaml) + + self.assertEqual(context.exception.args[0], "CWL file shell #!/bin/bash does not match post.sh shell #!/bin/bashoo") #noqa + def test_parse_workflow_json(self): """Test parsing of workflow with a JSON input job file.""" cwl_wf_file = find("examples/clamr-ffmpeg-build/clamr_wf.cwl") @@ -76,6 +100,16 @@ def test_parse_workflow_no_job(self): for task in tasks: self.assertEqual(task.workflow_id, workflow_id) + def test_parse_workflow_missing_input(self): + """Test parsing a workflow with a missing input value in the input file.""" + cwl_wf_file = find('ci/test_workflows/missing-input/workflow.cwl') + cwl_job_yaml = find('ci/test_workflows/missing-input/input.yml') + + workflow_id = generate_workflow_id() + + with self.assertRaises(CwlParseError): + _, _ = self.parser.parse_workflow(workflow_id, cwl_wf_file, cwl_job_yaml) + WORKFLOW_GOLD_SCRIPT = Workflow( name='clamr_wf', @@ -127,6 +161,65 @@ def test_parse_workflow_no_job(self): workflow_id=generate_workflow_id()) TASKS_GOLD_SCRIPT = [ + Task( + name='clamr', + base_command='/CLAMR/clamr_cpuonly', + hints=[Hint(class_='DockerRequirement', params={'dockerFile': '# Dockerfile.clamr-ffmpeg\n# Developed on Chicoma @lanl\n# Patricia Grubel \n\nFROM debian:11\n\n\nRUN apt-get update && \\\n apt-get install -y wget gnupg git cmake ffmpeg g++ make openmpi-bin libopenmpi-dev libpng-dev libpng16-16 libpng-tools imagemagick libmagickwand-6.q16-6 libmagickwand-6.q16-dev\n\nRUN git clone https://github.com/lanl/CLAMR.git\nRUN cd CLAMR && cmake . && make clamr_cpuonly\n', 'beeflow:containerName': 'clamr-ffmpeg'}), #noqa + Hint(class_='beeflow:ScriptRequirement', params={'enabled': True, 'pre_script': 'echo "Before run"', 'post_script': 'echo "After run"', 'shell': '/bin/bash'})], #noqa + requirements=[], + inputs=[StepInput(id='graphic_steps', type='int', value=None, default=None, + source='steps_between_graphics', prefix='-g', position=None, + value_from=None), + StepInput(id='graphics_type', type='string', value=None, default=None, + source='graphics_type', prefix='-G', position=None, value_from=None), + StepInput(id='grid_res', type='int', value=None, default=None, + source='grid_resolution', prefix='-n', position=None, value_from=None), + StepInput(id='max_levels', type='int', value=None, default=None, + source='max_levels', prefix='-l', position=None, value_from=None), + StepInput(id='output_steps', type='int', value=None, default=None, + source='steps_between_outputs', prefix='-i', position=None, + value_from=None), + StepInput(id='time_steps', type='int', value=None, default=None, + source='time_steps', prefix='-t', position=None, value_from=None)], + outputs=[StepOutput(id='clamr/clamr_stdout', type='stdout', value=None, + glob='clamr_stdout.txt'), + StepOutput(id='clamr/outdir', type='Directory', value=None, + glob='graphics_output/graph%05d.png'), + StepOutput(id='clamr/time_log', type='File', value=None, + glob='total_execution_time.log')], + stdout='clamr_stdout.txt', + stderr=None, + workflow_id=WORKFLOW_GOLD.id + ), + Task( + name='ffmpeg', + base_command='ffmpeg -y', + hints=[Hint(class_='DockerRequirement', params={'dockerFile': '# Dockerfile.clamr-ffmpeg\n# Developed on Chicoma @lanl\n# Patricia Grubel \n\nFROM debian:11\n\n\nRUN apt-get update && \\\n apt-get install -y wget gnupg git cmake ffmpeg g++ make openmpi-bin libopenmpi-dev libpng-dev libpng16-16 libpng-tools imagemagick libmagickwand-6.q16-6 libmagickwand-6.q16-dev\n\nRUN git clone https://github.com/lanl/CLAMR.git\nRUN cd CLAMR && cmake . && make clamr_cpuonly\n', 'beeflow:containerName': 'clamr-ffmpeg'})], # noqa + requirements=[], + inputs=[StepInput(id='ffmpeg_input', type='Directory', value=None, default=None, + source='clamr/outdir', prefix='-i', position=2, + value_from='$("/graph%05d.png")'), + StepInput(id='frame_rate', type='int', value=None, default=None, + source='frame_rate', prefix='-r', position=3, value_from=None), + StepInput(id='frame_size', type='string', value=None, default=None, + source='frame_size', prefix='-s', position=4, value_from=None), + StepInput(id='input_format', type='string', value=None, default=None, + source='input_format', prefix='-f', position=1, value_from=None), + StepInput(id='output_file', type='string', value=None, default=None, + source='output_filename', prefix=None, position=6, value_from=None), + StepInput(id='pixel_format', type='string', value=None, default=None, + source='pixel_format', prefix='-pix_fmt', position=5, value_from=None)], + outputs=[StepOutput(id='ffmpeg/movie', type='File', value=None, + glob='$(inputs.output_file)'), + StepOutput(id='ffmpeg/ffmpeg_stderr', type='stderr', value=None, + glob='ffmpeg_stderr.txt')], + stdout=None, + stderr='ffmpeg_stderr.txt', + workflow_id=WORKFLOW_GOLD.id) +] + + +TASKS_GOLD_VALIDATE_SCRIPT = [ Task( name='clamr', base_command='/CLAMR/clamr_cpuonly', @@ -247,7 +340,7 @@ def test_parse_workflow_no_job(self): name='cf', hints=[], requirements=[], - inputs={InputParameter(id='infile', type='File', value=None)}, + inputs={InputParameter(id='infile', type='File', value='infile')}, outputs={OutputParameter(id='ffmpeg_movie', type='File', value=None, source='ffmpeg/outfile'), OutputParameter(id='clamr_dir', type='File', value=None, source='clamr/outfile')}, workflow_id=generate_workflow_id()) diff --git a/beeflow/tests/test_wf_interface.py b/beeflow/tests/test_wf_interface.py index 40034a8eb..84d9d53e5 100644 --- a/beeflow/tests/test_wf_interface.py +++ b/beeflow/tests/test_wf_interface.py @@ -6,7 +6,7 @@ from beeflow.common.wf_data import (Workflow, Task, Requirement, Hint, InputParameter, OutputParameter, StepInput, StepOutput, generate_workflow_id) from beeflow.common.wf_interface import WorkflowInterface -from beeflow.tests.mocks import MockGDBInterface +from beeflow.tests.mocks import MockGDBDriver class TestWorkflowInterface(unittest.TestCase): @@ -15,13 +15,18 @@ class TestWorkflowInterface(unittest.TestCase): @classmethod def setUpClass(cls): """Start the GDB and initialize the Workflow interface.""" - mock_gdb_iface = MockGDBInterface() - cls.wfi = WorkflowInterface(mock_gdb_iface) + mock_gdb_driver = MockGDBDriver() + cls.wfi = WorkflowInterface(None, mock_gdb_driver) def tearDown(self): """Clear all data in the Neo4j database.""" - if self.wfi.workflow_initialized() and self.wfi.workflow_loaded(): - self.wfi.finalize_workflow() + self.wfi._gdb_driver.workflow = None + self.wfi._gdb_driver.workflow_state = None + self.wfi._gdb_driver.tasks.clear() + self.wfi._gdb_driver.task_states.clear() + self.wfi._gdb_driver.task_metadata.clear() + self.wfi._gdb_driver.inputs.clear() + self.wfi._gdb_driver.outputs.clear() def test_initialize_workflow(self): """Test workflow initialization. @@ -131,17 +136,6 @@ def test_reset_workflow(self): for task in gdb_tasks: self.assertEqual(task.workflow_id, new_workflow_id) - def test_finalize_workflow(self): - """Test workflow deletion from the graph database.""" - self.wfi.initialize_workflow(Workflow( - "test_workflow", None, None, - [InputParameter("test_input", "File", "input.txt")], - [OutputParameter("test_output", "File", "output.txt", "viz/output")], - generate_workflow_id())) - self.wfi.finalize_workflow() - - self.assertFalse(self.wfi.workflow_loaded()) - def test_add_task(self): """Test task creation.""" task_name = "test_task" @@ -174,7 +168,9 @@ def test_add_task(self): stderr=stderr, workflow_id=workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + + self.wfi.add_task(task, task_state) # Task object assertions self.assertEqual(task_name, task.name) @@ -231,7 +227,9 @@ def test_restart_task(self): stderr=stderr, workflow_id=workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + + self.wfi.add_task(task, task_state) # Restart the task, should create a new Task new_task = self.wfi.restart_task(task, test_checkpoint_file) @@ -328,7 +326,9 @@ def test_get_task_by_id(self): stderr=stderr, workflow_id=workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + + self.wfi.add_task(task, task_state) self.assertEqual(task, self.wfi.get_task_by_id(task.id)) @@ -441,9 +441,11 @@ def test_get_task_state(self): None)], [StepOutput("test_task/output", "File", "output.txt", "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" - # Should be WAITING because workflow not yet executed + self.wfi.add_task(task, task_state) + + # Should be WAITING self.assertEqual("WAITING", self.wfi.get_task_state(task)) def test_set_task_state(self): @@ -460,7 +462,8 @@ def test_set_task_state(self): None)], [StepOutput("test_task/output", "File", "output.txt", "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + self.wfi.add_task(task, task_state) self.wfi.set_task_state(task, "RUNNING") @@ -481,7 +484,8 @@ def test_get_task_metadata(self): None)], [StepOutput("test_task/output", "File", "output.txt", "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + self.wfi.add_task(task, task_state) metadata = {"cluster": "fog", "crt": "charliecloud", "container_md5": "67df538c1b6893f4276d10b2af34ccfe", "job_id": 1337} @@ -502,7 +506,8 @@ def test_set_task_metadata(self): None)], [StepOutput("test_task/output", "File", "output.txt", "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + self.wfi.add_task(task, task_state) metadata = {"cluster": "fog", "crt": "charliecloud", "container_md5": "67df538c1b6893f4276d10b2af34ccfe", "job_id": 1337} @@ -528,7 +533,8 @@ def test_get_task_input(self): None)], [StepOutput("test_task/output", "File", "output.txt", "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + self.wfi.add_task(task, task_state) self.assertEqual(task.inputs[0], self.wfi.get_task_input(task, "test_input")) @@ -545,7 +551,8 @@ def test_set_task_input(self): [StepInput("test_input", "File", None, "default.txt", "test_input", None, None, None)], [StepOutput("test_task/output", "File", "output.txt", "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + self.wfi.add_task(task, task_state) test_input = StepInput("test_input", "File", "input.txt", "default.txt", "test_input", None, None, None) @@ -566,7 +573,8 @@ def test_get_task_output(self): None)], [StepOutput("test_task/output", "File", "output.txt", "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + self.wfi.add_task(task, task_state) self.assertEqual(task.outputs[0], self.wfi.get_task_output(task, "test_task/output")) @@ -584,37 +592,13 @@ def test_set_task_output(self): None, None)], [StepOutput("test_task/output", "File", None, "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + self.wfi.add_task(task, task_state) test_output = StepOutput("test_task/output", "File", "output.txt", "output.txt") self.wfi.set_task_output(task, "test_task/output", "output.txt") self.assertEqual(test_output, self.wfi.get_task_output(task, "test_task/output")) - def test_evaluate_expression(self): - """Test the evaluation of an input/output expression.""" - workflow_id = generate_workflow_id() - self.wfi.initialize_workflow(Workflow( - "test_workflow", None, None, - [InputParameter("test_input", "File", "input.txt")], - [OutputParameter("test_output", "File", "output.txt", "test_task/output")], - workflow_id)) - task = Task( - "test_task", "ls", None, None, - [StepInput("test_input", "File", "input.txt", "default.txt", "test_input", None, None, - '$("test_" + inputs.test_input)')], - [StepOutput("test_task/output", "File", None, "$(inputs.test_input).bak")], - None, None, workflow_id) - self.wfi.add_task(task) - - test_input = StepInput("test_input", "string", "test_input.txt", "default.txt", - "test_input", None, None, '$("test_" + inputs.test_input)') - self.wfi.evaluate_expression(task, "test_input") - self.assertEqual(test_input, self.wfi.get_task_input(task, "test_input")) - - test_output = StepOutput("test_task/output", "File", None, "test_input.txt.bak") - self.wfi.evaluate_expression(task, "test_task/output", output=True) - self.assertEqual(test_output, self.wfi.get_task_output(task, "test_task/output")) - def test_workflow_completed(self): """Test determining if a workflow has completed.""" workflow_id = generate_workflow_id() @@ -630,7 +614,8 @@ def test_workflow_completed(self): [StepOutput("test_task/output", "File", "output.txt", "output.txt")], None, None, workflow_id) - self.wfi.add_task(task) + task_state = "WAITING" + self.wfi.add_task(task, task_state) # Workflow not completed self.assertFalse(self.wfi.workflow_completed()) @@ -641,47 +626,6 @@ def test_workflow_completed(self): # Workflow now completed self.assertTrue(self.wfi.workflow_completed()) - def test_workflow_initialized(self): - """Test determining if a workflow is initialized.""" - self.wfi.initialize_workflow(Workflow( - "test_workflow", None, None, - [InputParameter("test_input", "File", "input.txt")], - [OutputParameter("test_output", "File", "output.txt", "viz/output")], - generate_workflow_id())) - - # Workflow now initialized - self.assertTrue(self.wfi.workflow_initialized()) - - def test_workflow_loaded(self): - """Test determining if a workflow is loaded.""" - self.wfi.initialize_workflow(Workflow( - "test_workflow", None, None, - [InputParameter("test_input", "File", "input.txt")], - [OutputParameter("test_output", "File", "output.txt", "viz/output")], - generate_workflow_id())) - self.wfi.finalize_workflow() - - # Workflow not loaded - self.assertFalse(self.wfi.workflow_loaded()) - - self.wfi.initialize_workflow(Workflow( - "test_workflow", None, None, - [InputParameter("test_input", "File", "input.txt")], - [OutputParameter("test_output", "File", "output.txt", "viz/output")], - generate_workflow_id())) - - # Workflow now loaded - self.assertTrue(self.wfi.workflow_loaded()) - - def test_workflow_id(self): - """Test retrieving the workflow ID from the workflow interface.""" - self.assertEqual(self.wfi.workflow_id, self.wfi._workflow_id) - - # Set workflow_id to None so it's retrieved from database - self.wfi._workflow_id = None - - self.assertEqual(self.wfi.workflow_id, self.wfi._workflow_id) - def _create_test_tasks(self, workflow_id): """Create test tasks to reduce redundancy.""" # Remember that add_task uploads the task to the database as well as returns a Task @@ -734,8 +678,9 @@ def _create_test_tasks(self, workflow_id): workflow_id=workflow_id) ] + task_state = "WAITING" for task in tasks: - self.wfi.add_task(task) + self.wfi.add_task(task, task_state) return tasks diff --git a/beeflow/tests/test_wf_manager.py b/beeflow/tests/test_wf_manager.py index 0abc0443f..f46998183 100644 --- a/beeflow/tests/test_wf_manager.py +++ b/beeflow/tests/test_wf_manager.py @@ -9,7 +9,7 @@ from test_parser import WORKFLOW_GOLD, TASKS_GOLD from beeflow.wf_manager.wf_manager import create_app from beeflow.wf_manager.resources import wf_utils -from beeflow.tests.mocks import MockWFI, MockGDBInterface +from beeflow.tests.mocks import MockWFI, MockGDBDriver from beeflow.common.config_driver import BeeConfig as bc from beeflow.common.wf_interface import WorkflowInterface @@ -82,14 +82,10 @@ def delay(*pargs, **kwargs): def test_submit_workflow(client, mocker, teardown_workflow, temp_db): """Test submitting a workflow.""" mocker.patch('beeflow.wf_manager.resources.wf_list.init_workflow', new=MockTask) - mocker.patch('beeflow.wf_manager.resources.wf_list.dep_manager.create_image', - return_value=True) - mocker.patch('beeflow.wf_manager.resources.wf_list.dep_manager.start_gdb', return_value=True) - mocker.patch('beeflow.wf_manager.resources.wf_list.dep_manager.wait_gdb', return_value=True) - mocker.patch('beeflow.wf_manager.resources.wf_list.dep_manager.kill_gdb', return_value=True) mocker.patch('beeflow.common.wf_data.generate_workflow_id', return_value='42') mocker.patch('beeflow.wf_manager.resources.wf_utils.get_workflow_interface', - return_value=WorkflowInterface(MockGDBInterface())) + return_value=WorkflowInterface(MockGDBDriver())) + mocker.patch('subprocess.run', return_value=True) mocker.patch('beeflow.wf_manager.resources.wf_utils.get_db_path', temp_db.db_file) mocker.patch('beeflow.wf_manager.resources.wf_list.db_path', temp_db.db_file) @@ -113,11 +109,6 @@ def test_submit_workflow(client, mocker, teardown_workflow, temp_db): def test_reexecute_workflow(client, mocker, teardown_workflow, temp_db): """Test reexecuting a workflow.""" mocker.patch('beeflow.wf_manager.resources.wf_list.init_workflow', new=MockTask) - mocker.patch('beeflow.wf_manager.resources.wf_list.dep_manager.create_image', - return_value=True) - mocker.patch('beeflow.wf_manager.resources.wf_list.dep_manager.start_gdb', return_value=True) - mocker.patch('beeflow.wf_manager.resources.wf_list.dep_manager.wait_gdb', return_value=True) - mocker.patch('beeflow.wf_manager.resources.wf_list.dep_manager.kill_gdb', return_value=True) mocker.patch('beeflow.wf_manager.resources.wf_utils.get_workflow_interface', return_value=MockWFI()) mocker.patch('beeflow.wf_manager.resources.wf_utils.get_db_path', temp_db.db_file) @@ -170,6 +161,7 @@ def test_start_workflow(client, mocker, temp_db): mocker.patch('beeflow.wf_manager.resources.wf_utils.update_wf_status', return_value=None) mocker.patch('beeflow.wf_manager.resources.wf_utils.get_db_path', new=lambda: temp_db.db_file) mocker.patch('beeflow.wf_manager.resources.wf_actions.db_path', temp_db.db_file) + mocker.patch('beeflow.common.wf_interface.WorkflowInterface.get_workflow_state', 'Waiting') resp = client().post(f'/bee_wfm/v1/jobs/{WF_ID}') assert resp.status_code == 200 @@ -181,11 +173,9 @@ def test_workflow_status(client, mocker, setup_teardown_workflow, temp_db): mocker.patch('beeflow.wf_manager.resources.wf_utils.get_db_path', temp_db.db_file) mocker.patch('beeflow.wf_manager.resources.wf_actions.db_path', temp_db.db_file) wf_name = 'wf' - bolt_port = 3030 - http_port = 3333 - https_port = 3455 + workdir = 'dir' - temp_db.workflows.init_workflow(WF_ID, wf_name, 'dir', bolt_port, http_port, https_port) + temp_db.workflows.init_workflow(WF_ID, wf_name, workdir) temp_db.workflows.add_task(123, WF_ID, 'task', "WAITING") temp_db.workflows.add_task(124, WF_ID, 'task', "RUNNING") @@ -202,14 +192,11 @@ def test_cancel_workflow(client, mocker, setup_teardown_workflow, temp_db): mocker.patch('beeflow.wf_manager.resources.wf_actions.db_path', temp_db.db_file) wf_name = 'wf' - wf_status = 'Pending' - bolt_port = 3030 - gdb_pid = 12345 + workdir = 'dir' - temp_db.workflows.init_workflow(WF_ID, wf_name, wf_status, 'dir', bolt_port, gdb_pid) + temp_db.workflows.init_workflow(WF_ID, wf_name, workdir) temp_db.workflows.add_task(123, WF_ID, 'task', "WAITING") temp_db.workflows.add_task(124, WF_ID, 'task', "RUNNING") - mocker.patch('beeflow.wf_manager.resources.wf_actions.dep_manager.kill_gdb', return_value=None) request = {'wf_id': WF_ID, 'option': 'cancel'} resp = client().delete(f'/bee_wfm/v1/jobs/{WF_ID}', json=request) @@ -225,14 +212,11 @@ def test_remove_workflow(client, mocker, setup_teardown_workflow, temp_db): mocker.patch('beeflow.wf_manager.resources.wf_actions.db_path', temp_db.db_file) wf_name = 'wf' - wf_status = 'Archived' - bolt_port = 3030 - gdb_pid = 12345 + workdir = 'dir' - temp_db.workflows.init_workflow(WF_ID, wf_name, wf_status, 'dir', bolt_port, gdb_pid) + temp_db.workflows.init_workflow(WF_ID, wf_name, workdir) temp_db.workflows.add_task(123, WF_ID, 'task', "WAITING") temp_db.workflows.add_task(124, WF_ID, 'task', "RUNNING") - mocker.patch('beeflow.wf_manager.resources.wf_actions.dep_manager.kill_gdb', return_value=None) request = {'wf_id': WF_ID, 'option': 'remove'} resp = client().delete(f'/bee_wfm/v1/jobs/{WF_ID}', json=request) diff --git a/beeflow/wf_manager/common/dep_manager.py b/beeflow/wf_manager/common/dep_manager.py deleted file mode 100755 index c9dbbfc43..000000000 --- a/beeflow/wf_manager/common/dep_manager.py +++ /dev/null @@ -1,225 +0,0 @@ -#!/usr/bin/env python3 - -"""Functions for managing the BEE depency container and associated bind mounts.""" - -import os -import re -import time -import shutil -import signal -import subprocess - -from beeflow.common import log as bee_logging -from beeflow.wf_manager.resources import wf_utils -from beeflow.common.config_driver import BeeConfig as bc - - -dep_log = bee_logging.setup(__name__) - - -class NoContainerRuntime(Exception): - """An exception for no container runtime like charliecloud or singularity.""" - - -def check_container_runtime(): - """Check if the container runtime is currently installed.""" - # Needs to support singuarity as well - if shutil.which("ch-convert") is None or shutil.which("ch-run") is None: - dep_log.error("ch-convert or ch-run not found. Charliecloud required" - " for neo4j container.") - raise NoContainerRuntime('') - - -def make_dep_dir(): - """Make a new bee dependency container directory.""" - bee_workdir = wf_utils.get_bee_workdir() - bee_dir = f'{bee_workdir}/deps' - bee_dir_exists = os.path.isdir(bee_dir) - if not bee_dir_exists: - os.makedirs(bee_dir) - - -def get_dep_dir(): - """Return the dependency directory path.""" - bee_workdir = wf_utils.get_bee_workdir() - bee_container_dir = f'{bee_workdir}/deps/' - return bee_container_dir - - -def get_container_dir(): - """Return the depency container path.""" - container_name = 'dep_container' - return get_dep_dir() + container_name - - -def check_container_dir(): - """Return true if the container directory exists.""" - container_dir = get_container_dir() - container_dir_exists = os.path.isdir(container_dir) - return container_dir_exists - - -def setup_gdb_mounts(mount_dir): - """Set up mount directories for the graph database.""" - data_dir = mount_dir + '/data' - logs_dir = mount_dir + '/logs' - run_dir = mount_dir + '/run' - certs_dir = mount_dir + '/certificates' - - data_dir = os.path.join(data_dir, "data") - os.makedirs(data_dir, exist_ok=True) - - logs_dir = os.path.join(logs_dir, "logs") - os.makedirs(logs_dir, exist_ok=True) - - mount_dir = os.path.join(run_dir, "run") - os.makedirs(mount_dir, exist_ok=True) - - gdb_certs_path = os.path.join(certs_dir, "certificates") - os.makedirs(gdb_certs_path, exist_ok=True) - - -def setup_gdb_configs(mount_dir, bolt_port, http_port, https_port): - """Set up GDB configuration. - - This function needs to be run before each new invocation since the - config file could have changed. - """ - container_path = get_container_dir() - confs_dir = os.path.join(mount_dir, "conf") - os.makedirs(confs_dir, exist_ok=True) - gdb_configfile = shutil.copyfile(container_path + "/var/lib/neo4j/conf/neo4j.conf", - confs_dir + "/neo4j.conf") - dep_log.debug(gdb_configfile) - - with open(gdb_configfile, "rt", encoding="utf8") as cfile: - data = cfile.read() - - bolt_config = r'#(dbms.connector.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]*' - data = re.sub(http_config, rf'\1:{http_port}', data) - https_config = r'#(dbms.connector.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) - - -def create_image(): - """Create a new BEE dependency container if one does not exist. - - By default, the container is stored in /tmp//beeflow/deps. - """ - # Can throw an exception that needs to be handled by the caller - check_container_runtime() - - dep_img = bc.get('DEFAULT', 'neo4j_image') - - # Check for BEE dependency container directory: - container_dir_exists = check_container_dir() - if container_dir_exists: - dep_log.info('Already have neo4j container') - return - - make_dep_dir() - container_dir = get_container_dir() - # Build new dependency container - try: - subprocess.run(["ch-convert", "-i", "tar", "-o", "dir", - str(dep_img), str(container_dir)], check=True) - except subprocess.CalledProcessError as error: - dep_log.error(f"ch-convert failed: {error}") - shutil.rmtree(container_dir) - dep_log.debug(f"GraphDB container mount directory {container_dir} removed") - return - - # Make the certificates directory - container_certs_path = os.path.join(container_dir, 'var/lib/neo4j/certificates') - os.makedirs(container_certs_path, exist_ok=True) - - -def start_gdb(mount_dir, bolt_port, http_port, https_port, reexecute=False): - """Start the graph database.""" - setup_gdb_configs(mount_dir, bolt_port, http_port, https_port) - # We need to rerun the mount step before each start - if not reexecute: - setup_gdb_mounts(mount_dir) - - db_password = bc.get('graphdb', 'dbpass') - data_dir = mount_dir + '/data' - logs_dir = mount_dir + '/logs' - run_dir = mount_dir + '/run' - certs_dir = mount_dir + '/certificates' - confs_dir = mount_dir + "/conf" - - container_path = get_container_dir() - if not reexecute: - try: - command = ['neo4j-admin', 'set-initial-password', str(db_password)] - subprocess.run([ - "ch-run", - "--set-env=" + container_path + "/ch/environment", - "-b", confs_dir + ":/var/lib/neo4j/conf", - "-b", data_dir + ":/data", - "-b", logs_dir + ":/logs", - "-b", run_dir + ":/var/lib/neo4j/run", container_path, - "--", *command - ], check=True) - except subprocess.CalledProcessError: - dep_log.error("neo4j-admin set-initial-password failed") - return -1 - - try: - command = ['neo4j', 'start'] - with subprocess.Popen(["ch-run", - "--set-env=" + container_path + "/ch/environment", - "-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", - container_path, - "--", *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) - return pid - except FileNotFoundError: - dep_log.error("Neo4j failed to start.") - return -1 - - -def wait_gdb(log): - """Need to wait for the GDB. Currently, we're using the sleep time paramater. - - We'd like to remove that in the future. - """ - gdb_sleep_time = bc.get('graphdb', 'sleep_time') - log.info(f'waiting {gdb_sleep_time}s for GDB to come up') - time.sleep(gdb_sleep_time) - - -def remove_gdb(): - """Remove the current GDB bind mount directory.""" - bee_workdir = wf_utils.get_bee_workdir() - gdb_workdir = os.path.join(bee_workdir, 'current_gdb') - old_gdb_workdir = os.path.join(bee_workdir, 'old_gdb') - if os.path.isdir(gdb_workdir): - # Rename the directory to guard against NFS errors - shutil.move(gdb_workdir, old_gdb_workdir) - time.sleep(2) - shutil.rmtree(old_gdb_workdir) - time.sleep(2) - - -def kill_gdb(pid): - """Kill the GDB with the associated pid.""" - try: - os.kill(pid, signal.SIGTERM) - except OSError: - dep_log.info('Process already killed') diff --git a/beeflow/wf_manager/resources/wf_actions.py b/beeflow/wf_manager/resources/wf_actions.py index d19e54ea7..30b0d6285 100644 --- a/beeflow/wf_manager/resources/wf_actions.py +++ b/beeflow/wf_manager/resources/wf_actions.py @@ -9,7 +9,6 @@ from beeflow.common.db import wfm_db from beeflow.common.db.bdb import connect_db -from beeflow.wf_manager.common import dep_manager log = bee_logging.setup(__name__) db_path = wf_utils.get_db_path() @@ -61,14 +60,10 @@ def delete(self, wf_id): if option == "cancel": wfi = wf_utils.get_workflow_interface(wf_id) # Remove all tasks currently in the database - if wfi.workflow_loaded(): - wfi.finalize_workflow() + wfi.set_workflow_state('Cancelled') wf_utils.update_wf_status(wf_id, 'Cancelled') db.workflows.update_workflow_state(wf_id, 'Cancelled') - log.info("Workflow cancelled") - log.info("Shutting down gdb") - pid = db.workflows.get_gdb_pid(wf_id) - dep_manager.kill_gdb(pid) + log.info(f"Workflow {wf_id} cancelled") resp = make_response(jsonify(status='Cancelled'), 202) elif option == "remove": log.info(f"Removing workflow {wf_id}.") @@ -89,12 +84,13 @@ def patch(self, wf_id): option = self.reqparse.parse_args()['option'] wfi = wf_utils.get_workflow_interface(wf_id) + log.info('Pausing/resuming workflow') wf_state = wfi.get_workflow_state() - if option == 'pause' and wf_state == 'RUNNING': + if option == 'pause' and wf_state in ('RUNNING', 'INITIALIZING'): wfi.pause_workflow() wf_utils.update_wf_status(wf_id, 'Paused') db.workflows.update_workflow_state(wf_id, 'Paused') - log.info("Workflow Paused") + log.info(f"Workflow {wf_id} Paused") resp = make_response(jsonify(status='Workflow Paused'), 200) elif option == 'resume' and wf_state == 'PAUSED': wfi.resume_workflow() @@ -102,7 +98,7 @@ def patch(self, wf_id): wf_utils.schedule_submit_tasks(wf_id, tasks) wf_utils.update_wf_status(wf_id, 'Running') db.workflows.update_workflow_state(wf_id, 'Running') - log.info("Workflow Resumed") + log.info(f"Workflow {wf_id} Resumed") resp = make_response(jsonify(status='Workflow Resumed'), 200) else: resp_msg = f'Cannot {option} workflow. It is currently {wf_state.lower()}.' diff --git a/beeflow/wf_manager/resources/wf_list.py b/beeflow/wf_manager/resources/wf_list.py index ea30b2d4f..e188bb7ff 100644 --- a/beeflow/wf_manager/resources/wf_list.py +++ b/beeflow/wf_manager/resources/wf_list.py @@ -16,7 +16,6 @@ # from beeflow.common.wf_profiler import WorkflowProfiler from beeflow.wf_manager.resources import wf_utils -from beeflow.wf_manager.common import dep_manager from beeflow.common import wf_data from beeflow.common.db import wfm_db @@ -35,67 +34,28 @@ # wf_profiler = WorkflowProfiler(wf_name, output_path) -def extract_wf(wf_id, filename, workflow_archive, reexecute=False): +def extract_wf(wf_id, filename, workflow_archive): """Extract a workflow into the workflow directory.""" wf_utils.create_workflow_dir(wf_id) wf_dir = wf_utils.get_workflow_dir(wf_id) archive_path = os.path.join(wf_dir, filename) workflow_archive.save(archive_path) - if not reexecute: - subprocess.run(['tar', '-xf', archive_path, '-C', wf_dir], check=False) - cwl_dir = os.path.join(wf_dir, filename.split('.')[0]) - return cwl_dir + cwl_dir = wf_dir + "/cwl_files" - subprocess.run(['tar', '-xf', archive_path, '--strip-components=1', - '-C', wf_dir], check=False) - archive_dir = os.path.join(wf_dir, 'gdb') - return archive_dir + os.mkdir(cwl_dir) + subprocess.run(['tar', '-xf', archive_path, '--strip-components=1', '-C', cwl_dir], + check=False) + return cwl_dir @shared_task(ignore_result=True) -def init_workflow(wf_id, wf_name, wf_dir, wf_workdir, bolt_port, http_port, - https_port, no_start, workflow=None, tasks=None, reexecute=False): +def init_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, workflow=None, + tasks=None): """Initialize the workflow in a separate process.""" - print('Initializing GDB and workflow...') - try: - dep_manager.create_image() - except dep_manager.NoContainerRuntime: - crt_message = "Charliecloud not installed in current environment." - log.error(crt_message) - return - - gdb_pid = dep_manager.start_gdb(wf_dir, bolt_port, http_port, https_port, reexecute=reexecute) - dep_manager.wait_gdb(log) - - wfi = wf_utils.get_workflow_interface_by_bolt_port(bolt_port) - if reexecute: - wfi.reset_workflow(wf_id) - else: - wfi.initialize_workflow(workflow) - - # initialize_wf_profiler(wf_name) - - log.info('Setting workflow metadata') - wf_utils.create_wf_metadata(wf_id, wf_name) db = connect_db(wfm_db, db_path) - if reexecute: - _, tasks = wfi.get_workflow() - for task in tasks: - wfi.add_task(task) - metadata = wfi.get_task_metadata(task) - metadata['workdir'] = wf_workdir - wfi.set_task_metadata(task, metadata) - db.workflows.add_task(task.id, wf_id, task.name, "WAITING") - - db.workflows.update_gdb_pid(wf_id, gdb_pid) - wf_utils.update_wf_status(wf_id, 'Waiting') - db.workflows.update_workflow_state(wf_id, 'Waiting') - if no_start: - log.info('Not starting workflow, as requested') - else: - log.info('Starting workflow') - db.workflows.update_workflow_state(wf_id, 'Running') - wf_utils.start_workflow(wf_id) + wf_utils.connect_neo4j_driver(db.info.get_port('bolt')) + wf_utils.setup_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, + workflow, tasks) db_path = wf_utils.get_db_path() @@ -118,7 +78,7 @@ def get(self): return resp def post(self): - """Upload a workflow, initialize database, and start if required.""" + """Upload a workflown and start.""" db = connect_db(wfm_db, db_path) reqparser = reqparse.RequestParser() reqparser.add_argument('wf_name', type=str, required=True, @@ -148,18 +108,16 @@ def post(self): wf_id = workflow.id wf_dir = extract_wf(wf_id, wf_filename, wf_tarball) - bolt_port = wf_utils.get_open_port() - http_port = wf_utils.get_open_port() - https_port = wf_utils.get_open_port() - db.workflows.init_workflow(wf_id, wf_name, wf_dir, bolt_port, http_port, https_port) - init_workflow.delay(wf_id, wf_name, wf_dir, wf_workdir, bolt_port, http_port, - https_port, no_start, workflow=workflow, tasks=tasks) + db.workflows.init_workflow(wf_id, wf_name, wf_dir) + + init_workflow.delay(wf_id, wf_name, wf_dir, wf_workdir, + no_start, workflow=workflow, tasks=tasks) return make_response(jsonify(msg='Workflow uploaded', status='ok', wf_id=wf_id), 201) - def put(self): + def put(self): # This method can be deleted / deprecated """Reexecute a workflow.""" db = connect_db(wfm_db, db_path) reqparser = reqparse.RequestParser() @@ -177,25 +135,13 @@ def put(self): wf_name = data['wf_name'] wf_workdir = data['workdir'] - try: - dep_manager.create_image() - except dep_manager.NoContainerRuntime: - crt_message = "Charliecloud not installed in current environment." - log.error(crt_message) - resp = make_response(jsonify(msg=crt_message, status='error'), 418) - return resp - wf_id = wf_data.generate_workflow_id() - wf_dir = extract_wf(wf_id, wf_filename, workflow_archive, reexecute=True) - bolt_port = wf_utils.get_open_port() - http_port = wf_utils.get_open_port() - https_port = wf_utils.get_open_port() + wf_dir = extract_wf(wf_id, wf_filename, workflow_archive) - db.workflows.init_workflow(wf_id, wf_name, wf_dir, bolt_port, http_port, https_port) - init_workflow.delay(wf_id, wf_name, wf_dir, wf_workdir, bolt_port, http_port, - https_port, no_start=False, reexecute=True) + db.workflows.init_workflow(wf_id, wf_name, wf_dir) + init_workflow.delay(wf_id, wf_name, wf_dir, wf_workdir, no_start=False) - # Return the wf_id and created + # Returnid and created resp = make_response(jsonify(msg='Workflow uploaded', status='ok', wf_id=wf_id), 201) return resp diff --git a/beeflow/wf_manager/resources/wf_update.py b/beeflow/wf_manager/resources/wf_update.py index 8e557a163..6202e32f7 100644 --- a/beeflow/wf_manager/resources/wf_update.py +++ b/beeflow/wf_manager/resources/wf_update.py @@ -10,26 +10,26 @@ from flask import make_response, jsonify from flask_restful import Resource, reqparse from beeflow.wf_manager.resources import wf_utils -from beeflow.wf_manager.common import dep_manager from beeflow.common import log as bee_logging from beeflow.common.db import wfm_db from beeflow.common.db.bdb import connect_db - +from beeflow.common.config_driver import BeeConfig as bc log = bee_logging.setup(__name__) db_path = wf_utils.get_db_path() -def archive_workflow(db, wf_id): +def archive_workflow(db, wf_id, final_state=None): """Archive a workflow after completion.""" # Archive Config workflow_dir = wf_utils.get_workflow_dir(wf_id) shutil.copyfile(os.path.expanduser("~") + '/.config/beeflow/bee.conf', workflow_dir + '/' + 'bee.conf') - db.workflows.update_workflow_state(wf_id, 'Archived') - wf_utils.update_wf_status(wf_id, 'Archived') + wf_state = f'Archived/{final_state}' if final_state is not None else 'Archived' + db.workflows.update_workflow_state(wf_id, wf_state) + wf_utils.update_wf_status(wf_id, wf_state) bee_workdir = wf_utils.get_bee_workdir() archive_dir = os.path.join(bee_workdir, 'archives') @@ -38,6 +38,27 @@ def archive_workflow(db, wf_id): # We use tar directly since tarfile is apparently very slow workflows_dir = wf_utils.get_workflows_dir() subprocess.call(['tar', '-czf', archive_path, wf_id], cwd=workflows_dir) + remove_wf_dir = bc.get('DEFAULT', 'delete_completed_workflow_dirs') + if remove_wf_dir: + log.info('Removing Workflow Directory') + wf_utils.remove_wf_dir(wf_id) + + +def archive_fail_workflow(db, wf_id): + """Archive and fail a workflow.""" + archive_workflow(db, wf_id, final_state='Failed') + + +def set_dependent_tasks_dep_fail(db, wfi, wf_id, task): + """Recursively set all dependent task states of this task to DEP_FAIL.""" + # List of tasks whose states have already been updated + set_tasks = [task] + while len(set_tasks) > 0: + dep_tasks = wfi.get_dependent_tasks(set_tasks.pop()) + for dep_task in dep_tasks: + wfi.set_task_state(dep_task, 'DEP_FAIL') + db.workflows.update_task_state(dep_task.id, wf_id, 'DEP_FAIL') + set_tasks.extend(dep_tasks) class WFUpdate(Resource): @@ -46,70 +67,60 @@ class WFUpdate(Resource): def __init__(self): """Set up arguments.""" self.reqparse = reqparse.RequestParser() - self.reqparse.add_argument('wf_id', type=str, location='json', - required=True) - self.reqparse.add_argument('task_id', type=str, location='json', - required=True) - self.reqparse.add_argument('job_state', type=str, location='json', - required=True) - self.reqparse.add_argument('metadata', type=str, location='json', - required=False) - self.reqparse.add_argument('task_info', type=str, location='json', - required=False) - self.reqparse.add_argument('output', location='json', required=False) + self.reqparse.add_argument('state_updates', type=str, location='json', required=True) def put(self): - """Update the state of a task from the task manager.""" + """Do a batch update of task states from the task manager.""" db = connect_db(wfm_db, db_path) data = self.reqparse.parse_args() - wf_id = data['wf_id'] - task_id = data['task_id'] - job_state = data['job_state'] + state_updates = jsonpickle.decode(data['state_updates']) - wfi = wf_utils.get_workflow_interface(wf_id) - task = wfi.get_task_by_id(task_id) - wfi.set_task_state(task, job_state) - db.workflows.update_task_state(task_id, wf_id, job_state) + for state_update in state_updates: + self.update_task_state(state_update, db) - # Get metadata from update if available - if 'metadata' in data: - if data['metadata'] is not None: - metadata = jsonpickle.decode(data['metadata']) - wfi.set_task_metadata(task, metadata) + return make_response(jsonify(status=('Tasks updated successfully')), 200) + def handle_metadata(self, state_update, task, wfi): + """Handle metadata for a task update.""" bee_workdir = wf_utils.get_bee_workdir() + + # Get metadata from update if available + if state_update.metadata is not None: + old_metadata = wfi.get_task_metadata(task) + old_metadata.update(state_update.metadata) + wfi.set_task_metadata(task, old_metadata) + # Get output from the task - if 'metadata' in data: - if data['metadata'] is not None: - metadata = jsonpickle.decode(data['metadata']) - old_metadata = wfi.get_task_metadata(task) - old_metadata.update(metadata) - wfi.set_task_metadata(task, old_metadata) - - if 'output' in data and data['output'] is not None: + if state_update.output is not None: fname = f'{wfi.workflow_id}_{task.id}_{int(time.time())}.json' task_output_path = os.path.join(bee_workdir, fname) with open(task_output_path, 'w', encoding='utf8') as fp: - json.dump(json.loads(data['output']), fp, indent=4) + json.dump(state_update.output, fp, indent=4) + + def handle_checkpoint_restart(self, state_update, task, wfi, db): + """Handle checkpoint restart for a task update. - if 'task_info' in data and data['task_info'] is not None: - task_info = jsonpickle.decode(data['task_info']) - checkpoint_file = task_info['checkpoint_file'] + Returns True if a checkpoint-restart was done, else False (indicating + that more state handling is necessary). + """ + if state_update.task_info is not None: + checkpoint_file = state_update.task_info['checkpoint_file'] new_task = wfi.restart_task(task, checkpoint_file) if new_task is None: log.info('No more restarts') - wf_state = wfi.get_workflow_state() - wfi.set_workflow_state('Failed') - wf_utils.update_wf_status(wf_id, 'Failed') - db.workflows.update_workflow_state(wf_id, 'Failed') - return make_response(jsonify(status=f'Task {task_id} set to {job_state}')) - db.workflows.add_task(new_task.id, wf_id, new_task.name, "WAITING") + archive_fail_workflow(db, state_update.wf_id) + return True + db.workflows.add_task(new_task.id, state_update.wf_id, new_task.name, "WAITING") # Submit the restart task tasks = [new_task] - wf_utils.schedule_submit_tasks(wf_id, tasks) - return make_response(jsonify(status='Task {task_id} restarted')) - - if job_state in ('COMPLETED', 'FAILED'): + wf_utils.schedule_submit_tasks(state_update.wf_id, tasks) + log.info(f'Task {state_update.task_id} restarted') + return True + return False + + def handle_state_change(self, state_update, task, wfi, db): + """Handle a normal state change for a task.""" + if state_update.job_state == 'COMPLETED': for output in task.outputs: if output.glob is not None: wfi.set_task_output(task, output.id, output.glob) @@ -118,31 +129,34 @@ def put(self): tasks = wfi.finalize_task(task) wf_state = wfi.get_workflow_state() if tasks and wf_state != 'PAUSED': - wf_utils.schedule_submit_tasks(wf_id, tasks) + wf_utils.schedule_submit_tasks(state_update.wf_id, tasks) if wfi.workflow_completed(): - log.info("Workflow Completed") - wf_id = wfi.workflow_id - archive_workflow(db, wf_id) - pid = db.workflows.get_gdb_pid(wf_id) - dep_manager.kill_gdb(pid) - if wf_state == 'FAILED': - log.info("Workflow failed") - log.info("Shutting down GDB") wf_id = wfi.workflow_id - archive_workflow(db, wf_id) - pid = db.workflows.get_gdb_pid(wf_id) - dep_manager.kill_gdb(pid) - - if job_state == 'BUILD_FAIL': + log.info(f"Workflow {wf_id} Completed") + archive_workflow(db, state_update.wf_id) + log.info('Workflow Completed') + + # If the job failed and it doesn't include a checkpoint-restart hint, + # then fail the entire workflow + if state_update.job_state == 'FAILED': + set_dependent_tasks_dep_fail(db, wfi, state_update.wf_id, task) + log.info("Workflow failed") + wf_id = wfi.workflow_id + archive_fail_workflow(db, wf_id) + + if state_update.job_state == 'BUILD_FAIL': log.error(f'Workflow failed due to failed container build for task {task.name}') - wfi.set_workflow_state('Failed') - wf_utils.update_wf_status(wf_id, 'Failed') - db.workflows.update_workflow_state(wf_id, 'Failed') - - resp = make_response(jsonify(status=(f'Task {task_id} belonging to WF {wf_id} set to' - f'{job_state}')), 200) - return resp -# Ignoring C901,R0915: "'WFUPdate.put' is too complex" - this requires a refactor -# (or maybe the LOC limit is too low) -# pylama:ignore=C901,R0915 + archive_fail_workflow(db, state_update.wf_id) + + def update_task_state(self, state_update, db): + """Update the state of a single task from the task manager.""" + wfi = wf_utils.get_workflow_interface(state_update.wf_id) + task = wfi.get_task_by_id(state_update.task_id) + wfi.set_task_state(task, state_update.job_state) + db.workflows.update_task_state(state_update.task_id, state_update.wf_id, + state_update.job_state) + + self.handle_metadata(state_update, task, wfi) + if not self.handle_checkpoint_restart(state_update, task, wfi, db): + self.handle_state_change(state_update, task, wfi, db) diff --git a/beeflow/wf_manager/resources/wf_utils.py b/beeflow/wf_manager/resources/wf_utils.py index 5a7ad0fe8..efccb2ba5 100644 --- a/beeflow/wf_manager/resources/wf_utils.py +++ b/beeflow/wf_manager/resources/wf_utils.py @@ -2,20 +2,22 @@ import os import shutil -import socket import requests import jsonpickle from beeflow.common import log as bee_logging from beeflow.common.config_driver import BeeConfig as bc -from beeflow.common.gdb_interface import GraphDatabaseInterface -from beeflow.common.gdb.neo4j_driver import Neo4jDriver +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 from beeflow.common.db import wfm_db from beeflow.common.db.bdb import connect_db +from celery import shared_task #noqa (pylama can't find celery imports) + log = bee_logging.setup(__name__) @@ -111,6 +113,16 @@ def read_wf_status(wf_id): return wf_status +def read_wf_name(wf_id): + """Read workflow name metadata file.""" + bee_workdir = get_bee_workdir() + workflows_dir = os.path.join(bee_workdir, 'workflows', wf_id) + status_path = os.path.join(workflows_dir, 'bee_wf_name') + with open(status_path, 'r', encoding="utf8") as status: + wf_name = status.readline() + return wf_name + + def create_wf_namefile(wf_name, wf_id): """Create workflow name metadata file.""" bee_workdir = get_bee_workdir() @@ -124,23 +136,14 @@ def get_workflow_interface(wf_id): """Instantiate and return workflow interface object.""" db = connect_db(wfm_db, get_db_path()) # Wait for the GDB - if db.workflows.get_workflow_state(wf_id) == 'Initializing': - raise RuntimeError('Workflow is still initializing') - bolt_port = db.workflows.get_bolt_port(wf_id) - return get_workflow_interface_by_bolt_port(bolt_port) - -def get_workflow_interface_by_bolt_port(bolt_port): - """Return a workflow interface connection using just the bolt port.""" - try: - driver = Neo4jDriver(user="neo4j", bolt_port=bolt_port, - db_hostname=bc.get("graphdb", "hostname"), - password=bc.get("graphdb", "dbpass")) - iface = GraphDatabaseInterface(driver) - wfi = WorkflowInterface(iface) - except KeyError: - log.error('The default way to load WFI didnt work') - # wfi = WorkflowInterface() + # bolt_port = db.info.get_bolt_port() + # return get_workflow_interface_by_bolt_port(wf_id, bolt_port) + driver = neo4j_driver.Neo4jDriver() + bolt_port = db.info.get_port('bolt') + if bolt_port != -1: + connect_neo4j_driver(bolt_port) + wfi = WorkflowInterface(wf_id, driver) return wfi @@ -245,16 +248,6 @@ def submit_tasks_scheduler(tasks): return resp.json() -def get_open_port(): - """Return an open ephemeral port.""" - s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) - s.bind(("", 0)) - s.listen(1) - port = s.getsockname()[1] - s.close() - return port - - def schedule_submit_tasks(wf_id, tasks): """Schedule and then submit tasks to the TM.""" # Submit ready tasks to the scheduler @@ -263,6 +256,52 @@ def schedule_submit_tasks(wf_id, tasks): submit_tasks_tm(wf_id, tasks, allocation) +def connect_neo4j_driver(bolt_port): + """Create a neo4j driver to a gdb through bolt port.""" + driver = neo4j_driver.Neo4jDriver() + driver.connect(user="neo4j", bolt_port=bolt_port, + db_hostname=bc.get("graphdb", "hostname"), + password=bc.get("graphdb", "dbpass")) + driver.create_bee_node() + + +def setup_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, workflow=None, + tasks=None): + """Initialize Workflow in Separate Process.""" + wfi = get_workflow_interface(wf_id) + wfi.initialize_workflow(workflow) + + log.info('Setting workflow metadata') + create_wf_metadata(wf_id, wf_name) + db = connect_db(wfm_db, get_db_path()) + for task in tasks: + task_state = "" if no_start else "WAITING" + wfi.add_task(task, task_state) + metadata = wfi.get_task_metadata(task) + metadata['workdir'] = wf_workdir + wfi.set_task_metadata(task, metadata) + db.workflows.add_task(task.id, wf_id, task.name, task_state) + + if no_start: + update_wf_status(wf_id, 'No Start') + db.workflows.update_workflow_state(wf_id, 'No Start') + log.info('Not starting workflow, as requested') + else: + update_wf_status(wf_id, 'Waiting') + db.workflows.update_workflow_state(wf_id, 'Waiting') + log.info('Starting workflow') + db.workflows.update_workflow_state(wf_id, 'Running') + 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()) @@ -270,6 +309,13 @@ def start_workflow(wf_id): state = wfi.get_workflow_state() if state in ('RUNNING', 'PAUSED', 'COMPLETED'): return False + _, tasks = wfi.get_workflow() + tasks.reverse() + for task in tasks: + task_state = wfi.get_task_state(task) + if task_state == '': + wfi.set_task_state(task, 'WAITING') + db.workflows.update_task_state(task.id, wf_id, 'WAITING') wfi.execute_workflow() tasks = wfi.get_ready_tasks() schedule_submit_tasks(wf_id, tasks) diff --git a/beeflow/wf_manager/wf_manager.py b/beeflow/wf_manager/wf_manager.py index 5c3fcbdec..8134955a0 100644 --- a/beeflow/wf_manager/wf_manager.py +++ b/beeflow/wf_manager/wf_manager.py @@ -3,6 +3,7 @@ import os from flask import Flask from celery import Celery # noqa (pylama can't find celery imports) +from celery import shared_task #noqa from beeflow.common.api import BeeApi from beeflow.common import paths from beeflow.wf_manager.resources.wf_list import WFList @@ -34,6 +35,7 @@ def create_app(): }) celery_app.set_default() app.extensions['celery'] = celery_app + return app diff --git a/ci/README.md b/ci/README.md index 028a6bd58..ee811b045 100644 --- a/ci/README.md +++ b/ci/README.md @@ -1,9 +1,8 @@ # CI code This directory contains all the scripts that are needed for configuring and -running BEE on a CI machine. `BATCH_SCHEDULER` is set in the environment by the -workflow to either `Slurm` or `Flux`, which is then used in various places in -these scripts. The scripts are as follows: +running BEE on a CI machine. `BEE_WORKER` must be set in the environment by the +workflow to `Slurmrestd`, `SlurmCommands`, or `Flux`. The scripts are as follows: * `env.sh`: CI environment set up * `batch_scheduler.sh`: Install and set up a batch scheduler diff --git a/ci/batch_scheduler.sh b/ci/batch_scheduler.sh index a89e4c275..e92aa119b 100755 --- a/ci/batch_scheduler.sh +++ b/ci/batch_scheduler.sh @@ -1,14 +1,15 @@ #!/bin/sh # Set up and start the batch scheduler -case $BATCH_SCHEDULER in -Slurm) +case $BEE_WORKER in +Slurmrestd|SlurmCommands) ./ci/slurm_start.sh ;; Flux) ./ci/flux_install.sh ;; *) - printf "ERROR: Invalid batch scheduler '%s'\n" "$BATCH_SCHEDULER" + printf "ERROR: Invalid worker type '%s'\n" "$BEE_WORKER" + exit 1 ;; esac diff --git a/ci/bee_config.sh b/ci/bee_config.sh index 2241d34f1..5e8ae11e1 100755 --- a/ci/bee_config.sh +++ b/ci/bee_config.sh @@ -1,13 +1,21 @@ #!/bin/sh # BEE Configuration +case $BEE_WORKER in +Slurm*) + export WORKLOAD_SCHEDULER=Slurm + ;; +Flux) + export WORKLOAD_SCHEDULER=Flux + ;; +esac + mkdir -p $(dirname $BEE_CONFIG) cat >> $BEE_CONFIG <> $BEE_CONFIG <> $BEE_CONFIG <> $SLURM_CONF < + + + + + + + + + + + + + + + coverage + coverage + 69% + 69% + + diff --git a/docs/sphinx/bee_cwl.rst b/docs/sphinx/bee_cwl.rst index 62dc85de1..4e62b0db0 100644 --- a/docs/sphinx/bee_cwl.rst +++ b/docs/sphinx/bee_cwl.rst @@ -180,18 +180,21 @@ beeflow:ScriptRequirement Some tasks may require small additional commands for setup or teardown such as loading modules, setting up checkpointing files, or cleaning up after a run. The script requirement enables this by adding shell scripts that will run before -and after a task. The script must be within the workflow directory. The shell -interpreter will be set to whatever is in the ``$SHELL`` environment variable -on the system e.g. if ``$SHELL`` is ``/bin/bash``, it will run the script as -bash. The pre_script is run before a task and the post_script is run after. -Currently, we only support running scripts outside of a container. We are -considering adding container support in the future. +and after a task. The script must be within the workflow directory. The desired +shell interpreter must be specified in both the ``beeflow:ScriptRequirement`` section +of the cwl file as well as the shebang line of the script, otherwise, an error will be +returned. Furthermore, if different shell interpreters are specified, then expect +an error. Default shell environment variable is ``/bin/bash``. The pre_script is run +before a task and the post_script is run after. Currently, we only support running +scripts outside of a container. We are considering adding container support in the +future. ScriptRequirement currently supports the following options: * ``enabled`` - Enables pre/post script support * ``pre_script`` - Path to the pre_script relative to the workflow directory. * ``post_script`` - Path to the post_script relative to the workflow directory. +* ``shell`` - Desired shell interpreter. Must match shell interpreter defined in pre/post scripts. An example ``beeflow:ScriptRequirement`` is shown below:: @@ -199,3 +202,4 @@ An example ``beeflow:ScriptRequirement`` is shown below:: enabled: True pre_script: before.sh post_script: after.sh + shell: /bin/bash diff --git a/docs/sphinx/commands.rst b/docs/sphinx/commands.rst index 997714e6f..07ff348b5 100644 --- a/docs/sphinx/commands.rst +++ b/docs/sphinx/commands.rst @@ -18,11 +18,13 @@ Options: ``beeflow core status``: Check the status of beeflow and the components. -``beeflow core stop``: Stop the current running beeflow daemon. +``beeflow core info``: Get information about beeflow, including .beeflow directory location, log location, and version number. + +``beeflow core stop``: Stop running beeflow components. Active workflows will be paused. You may continue running paused workflows with the ``beeflow resume `` command. Once you start beeflow components after a stop, you should check the status of workflows, query any running workflows. If they were intializing when a ``beeflow core stop`` was issued, the workflow may be running with tasks stuck in the waiting state. If this occurs and you want the workflow to continue pause and resume the workflow (``beeflow pause ``, ``beeflow resume ``) or to start over cancel the workflow (``beeflow cancel ``) and resubmit it. ``beeflow core --version``: Display the version number of BEE. -``beeflow core reset``: Stop the beeflow daemon and cleanup the bee_workdir directory to start from a fresh install. +``beeflow core reset``: Stop the beeflow daemon and cleanup the bee_workdir directory to start from a fresh install. Options: ``--archive``, ``-a``, Backup logs, workflows, and containers in bee_workdir directory before removal. [optional] @@ -57,6 +59,11 @@ Arguments: ``beeflow package``: Package a workflow into a tarball. +Arguments: + - WF_PATH Path to the workflow package directory [required] + - PACKAGE_DEST Path for where the packaged workflow should be saved [required] + + Arguments: - WF_PATH, Path to the workflow package directory [required] - PACKAGE_DEST, Path for where the packaged workflow should be saved [required] @@ -95,6 +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/contribute.rst b/docs/sphinx/contribute.rst index 85bd3f4de..9dc2fa707 100644 --- a/docs/sphinx/contribute.rst +++ b/docs/sphinx/contribute.rst @@ -1,16 +1,16 @@ +.. _contribute: + Contribute ************ Git Workflow ============ -BEE has two lifetime branches, develop and main. All Pull Requests's (PR's) will be reviewed and tested then merged into develop when tests pass and review is complete. - -Upon release develop will be merged by the team lead into main. +BEE has two lifetime branches, develop and main. To work on a fix or feature, create a branch from develop. These branches should address an open issue and follow the format **issue#/title** (e.g. 'issue857/mpi-integration-test'). If there isn't an issue for your fix or feature consider making one. -Open a **work in progress** PR with label of **'WIP'** and link the PR to an issue using the term **'addresses'** issue #. +All pull requests (PR's) are made from feature or issue branches and undergo review and testing before they can be merged into develop. Open a **work in progress** PR with label of **'WIP'**. Before submitting the PR for approval, merge develop into your branch and fix any conflicts. Remove the 'WIP' label when the PR is complete and ready for final review. GitHub CI tests must pass before merging into develop. -Merge develop into your branch and fix conflicts before submitting a PR for approval. +Upon release, develop will be merged by the team lead into main. Additionally, all changes must pass overnight tests before being merged into main. Style Guide =========== diff --git a/docs/sphinx/development.rst b/docs/sphinx/development.rst index f0ef2aba6..e33c654b7 100644 --- a/docs/sphinx/development.rst +++ b/docs/sphinx/development.rst @@ -9,6 +9,12 @@ install them to a virtual environment. It also makes it easy to build and install our package locally as well as publish it to PyPI, obviating the need for a `setup.py` file. +Additional Poetry documentation: + +* https://poetry.eustace.io/docs/ + +* https://github.com/sdispater/poetry + Requirement: Python version 3.8 or greater ------------------------------------------ @@ -37,8 +43,6 @@ to: `[ $POETRY_ACTIVE ] || eval "$(pyenv init -)"` -Create a Virtual Environment and Install Dependencies ------------------------------------------------------ On MacOS, Poetry virtual environments are installed to `~/Library/Caches/pypoetry/virtualenvs`. To instead install to a local `.venv` directory, first run the command: @@ -46,32 +50,60 @@ To instead install to a local `.venv` directory, first run the command: When creating a Python virtual environment, Poetry will automatically install the version of Python of whatever `python` executable appears first on your PATH. -To create a Python 3.x virtual environment and install our project -dependencies (including developer dependencies): -`poetry install` +Development Workflow +==================== -To install without developer dependencies: +1. Make changes +--------------- +To work on a fix or feature, switch to the feature branch in the BEE repo (see :ref:`contribute`). -`poetry install --no-dev` +2. Create a Virtual Environment and Install Dependencies +--------------------------------------------------------- -This will also generate the package metadata in `beeflow.egg-info` (not tracked) and install -the package to your local system as a Python Egg. +After making your changes create a Python 3.x virtual environment and install our project +dependencies (including developer dependencies): +``poetry install`` + +3. Activate the Virtual Environment +----------------------------------- -Activate the Virtual Environment ------------------------------------------------------ To activate the virtual environment ('exit' or EOF to deactivate): -`poetry shell` +``poetry shell`` +4. Start the BEE components +--------------------------- -Run a Command in the Virtual Environment ------------------------------------------------------ -To run a command without activating the virtual environment: +``beeflow core start`` + +5. Test +--------- + +Test your new feature/fixes + +6. Commit Changes +----------------- + +If you're done making changes, follow the git workflow specified in :ref:`contribute`. + +7. Continue Development +----------------------- -`poetry run COMMAND [arguments]` +If you want to continue making changes, add them and then pause any running workflows: +``beeflow pause $ID`` + +Stop the bee components: + +``beeflow core stop`` + +Now you can repeat steps 2 to 5. + + +Dependency and Package Management with Poetry +============================================= Update Dependencies ----------------------------------------------------- @@ -113,20 +145,6 @@ Publish the Package to a Remote Repository `poetry publish` -Update Poetry ------------------------------------------------------ -To update Poetry: - -`poetry self:update` - -Additional Documentation ------------------------- -Additional documentation: - -* https://poetry.eustace.io/docs/ - -* https://github.com/sdispater/poetry - Running Tests ================== @@ -134,4 +152,9 @@ BEE includes unit and integration tests that can be run on a local system. To run the unit tests, make sure to install beeflow with ``poetry install -E cloud_extras``; the ``-E cloud_extras`` option forces Poetry to install extra dependencies required for some of the cloud API tests. After loading a shell with ``poetry shell``, you can run the unit tests with ``pytest beeflow/tests``. -For the integration tests, you'll first have to start beeflow with ``beeflow core start`` (see :ref:`command-line-interface`). Then, making sure that you have Charliecloud loaded in your environment, you can run ``./ci/integration_test.py`` to run the tests. The integration tests will create a directory ``~/.beeflow-integration`` to be used for storing temporary files as well as inspecting failure results. The script itself includes a number of options for running extra tests, details of which can be found through ``--help`` and other command line options. +For the integration tests, you'll first have to start beeflow with ``beeflow core start`` (see :ref:`command-line-interface`). Then, making sure that you have Charliecloud loaded in your environment, you can run ``./ci/integration_test.py`` to run the tests. This must be done from the root of BEE repository. The integration tests will create a directory ``~/.beeflow-integration`` to be used for storing temporary files as well as inspecting failure results. The script itself includes a number of options for running extra tests, details of which can be found through ``--help`` and other command line options. Running the script without any options will run the default test suite. Some tests are disabled by default due to runtime or environment constraints and need to be specified in a comma-separated list with ``--tests`` (``-t``) to be run. Run the script with just ``--show-tests`` (``-s``) to see a list of all possible tests. + +Git Workflow +================== + +See :ref:`contribute` for more information diff --git a/docs/sphinx/examples.rst b/docs/sphinx/examples.rst index a7ce5b357..252fa35f1 100644 --- a/docs/sphinx/examples.rst +++ b/docs/sphinx/examples.rst @@ -58,9 +58,9 @@ support all features. To run our simple example, you'll want to first create a workdir for the workflow and copy over the input file ``lorem.txt``. I'll refer to this path in -code samples as ``$WORKDIR_PATH``. Note that this is separate from the -directory containing the workflow itself, which contains all the CWL files and -the input YAML files. The workdir is where all of your input files should be +code samples as ``$WORKDIR_PATH``. Note that this ``$WORKDIR_PATH`` should be +located outside of the BEE repo. For example, it could be in your home +directory ``$HOME``. The workdir is where all of your input files should be stored before starting a workflow, as this will be the current working directory of all steps that are run. Output from each step will also be stored here. 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/index.rst b/docs/sphinx/index.rst index 688d216e1..e2bb733ba 100644 --- a/docs/sphinx/index.rst +++ b/docs/sphinx/index.rst @@ -21,9 +21,11 @@ error_logs contribute development - wf_api visualization +.. Commented out + wf_api + rest_api Indices and tables ================== diff --git a/docs/sphinx/installation.rst b/docs/sphinx/installation.rst index 3bad41f97..cb266ebd0 100644 --- a/docs/sphinx/installation.rst +++ b/docs/sphinx/installation.rst @@ -15,9 +15,9 @@ 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 3.5.x. We are currently using the latest version of Redis supplied on Docker Hub (as of 2023). + 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-3-5-17-ch.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. @@ -85,7 +85,9 @@ To check the status of the bee components run: .. code-block:: beeflow components: + redis ... RUNNING scheduler ... RUNNING + celery ... RUNNING slurmrestd ... RUNNING wf_manager ... RUNNING task_manager ... RUNNING diff --git a/docs/sphinx/rest_api.rst b/docs/sphinx/rest_api.rst new file mode 100644 index 000000000..21b69d0e1 --- /dev/null +++ b/docs/sphinx/rest_api.rst @@ -0,0 +1,27 @@ +BEEflow REST API +************************** + +This is a REST API for beeflow itself. It provides a way to remotely submit workflows to the system. +The REST API was created primarily for the purpose of connecting CI resources to beeflow, but could also be used to setup remote "workers". + +:module: beeflow.remote.remote +:show-refs: True + + +Endpoints +---------- +.. autofunction:: beeflow.remote.remote.get_wf_status + +.. autofunction:: beeflow.remote.remote.get_drop_point + +.. autofunction:: beeflow.remote.remote.get_owner + +.. autofunction:: beeflow.remote.remote.submit_new_wf + +.. autofunction:: beeflow.remote.remote.submit_new_wf_long + +.. autofunction:: beeflow.remote.remote.show_drops + +.. autofunction:: beeflow.remote.remote.cleanup_wf_directory + +.. autofunction:: beeflow.remote.remote.get_core_status 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. 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"^0.3.0" python-daemon = "^2.3.1" -gunicorn = "^20.1.0" +gunicorn = ">=20.1,<23.0" # typer version 0.6 and above seem to be throwing an AssertionError with no # attached info typer = "^0.5.0" # Seems to be required for Flux cffi = "^1.15.1" celery = { version = "^5.3.4", extras = ["redis", "sqlalchemy"] } +# Fix for poetry/docutils related bug +docutils = "0.18.1" # Cloud optional dependencies google-api-python-client = { version = "^2.66.0", optional = true } python-openstackclient = { version = "^6.0.0", optional = true } python-heatclient = { version = "^3.1.0", optional = true } +graphviz = "^0.20.3" [tool.poetry.extras] cloud_extras = ["google-api-python-client", "python-openstackclient", "python-heatclient"] @@ -89,6 +94,7 @@ pylama = "8.4.1" pylint = "2.15.9" pytest = "7.2.0" pytest-mock = "3.3.1" +pytest-cov = "5.0.0" # This is commented out until we can figure out why it's causing `poetry update` to loop forever sphinx = "^6" sphinx-rtd-theme = "^1.0"