From 13add9e1c669905478d5bed4c2bdf85f5cda4455 Mon Sep 17 00:00:00 2001 From: Krishna Kumar Date: Tue, 17 Oct 2023 15:42:28 -0500 Subject: [PATCH] DSJobs get job status --- .github/workflows/pytest.yml | 29 +++ .gitignore | 177 +++++++++++++ AUTHORS.md | 4 + LICENSE.md | 20 ++ README.md | 33 +++ dsjobs/__init__.py | 1 + dsjobs/jobs.py | 65 +++++ poetry.lock | 474 +++++++++++++++++++++++++++++++++++ pyproject.toml | 23 ++ tests/__init__.py | 0 tests/test_jobs.py | 37 +++ 11 files changed, 863 insertions(+) create mode 100644 .github/workflows/pytest.yml create mode 100644 .gitignore create mode 100644 AUTHORS.md create mode 100644 LICENSE.md create mode 100644 README.md create mode 100644 dsjobs/__init__.py create mode 100644 dsjobs/jobs.py create mode 100644 poetry.lock create mode 100644 pyproject.toml create mode 100644 tests/__init__.py create mode 100644 tests/test_jobs.py diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml new file mode 100644 index 0000000..2a4b311 --- /dev/null +++ b/.github/workflows/pytest.yml @@ -0,0 +1,29 @@ +name: Python Tests with Poetry + +on: [push, pull_request] +jobs: + ci: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - name: Install Python + uses: actions/setup-python@v4 + with: + python-version: '3.11' + # see details (matrix, python-version, python-version-file, etc.) + # https://github.com/actions/setup-python + - name: Install poetry + uses: abatilo/actions-poetry@v2 + - name: Setup a local virtual environment (if no poetry.toml file) + run: | + poetry config virtualenvs.create true --local + poetry config virtualenvs.in-project true --local + - uses: actions/cache@v3 + name: Define a cache for the virtual environment based on the dependencies lock file + with: + path: ./.venv + key: venv-${{ hashFiles('poetry.lock') }} + - name: Install the project dependencies + run: poetry install + - name: Run the automated tests (for example) + run: poetry run pytest -v \ No newline at end of file diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e2afc88 --- /dev/null +++ b/.gitignore @@ -0,0 +1,177 @@ +# OS temp files +**/.DS_Store* +*~* +*#* + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + + +# IntelliJ / PyCharm artifacts +.idea/ + +# VS Code artifacts +.vscode/ + +# Logs and databases +*.log +*.sqlite + diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 0000000..f823589 --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,4 @@ +# Authors + +* Prof. Pedro Arduino, University of Washington +* Krishna Kumar, University of Texas at Austin \ No newline at end of file diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..125f5b0 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,20 @@ +# MIT License +> Copyright (c) [2023] [Authors] + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000..03a7126 --- /dev/null +++ b/README.md @@ -0,0 +1,33 @@ +# DesignSafe Jobs + +[![PyTest](https://github.com/geoelements/dsapps/actions/workflows/pytest.yml/badge.svg)](https://github.com/geoelements/dsapps/actions/workflows/pytest.yml) +[![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/geoelements/dsjobs/main/LICENSE.md) + +`dsjobs` is a library that simplifies the process of submitting, running, and monitoring [TAPIS v2 / AgavePy](https://agavepy.readthedocs.io/en/latest/index.html) jobs on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org). + +## Installation + +Install `dsjobs` via pip (**coming soon**) + +```shell +pip3 install dsjobs +``` + +## Features + +* Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. `dsjobs` abstracts away the complexities. + +* Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment. + +## Support + +For any questions, issues, or feedback submit an [issue](https://github.com/geoelements/dsjobs/issues/new) + +## License + +`dsjobs` is licensed under the [MIT License](LICENSE.md). + +## Authors + +* Prof. Pedro Arduino, University of Washington +* Krishna Kumar, University of Texas at Austin \ No newline at end of file diff --git a/dsjobs/__init__.py b/dsjobs/__init__.py new file mode 100644 index 0000000..6c4a6fe --- /dev/null +++ b/dsjobs/__init__.py @@ -0,0 +1 @@ +from .jobs import get_status \ No newline at end of file diff --git a/dsjobs/jobs.py b/dsjobs/jobs.py new file mode 100644 index 0000000..a20dfdd --- /dev/null +++ b/dsjobs/jobs.py @@ -0,0 +1,65 @@ +import time +from datetime import datetime, timedelta, timezone +from tqdm import tqdm + +def get_status(ag, job_id, time_lapse=15): + """ + Retrieves and monitors the status of a job from Agave. + + This function initially waits for the job to start, displaying its progress using + a tqdm progress bar. Once the job starts, it monitors the job's status up to + a maximum duration specified by the job's "maxHours". If the job completes or fails + before reaching this maximum duration, it returns the job's final status. + + Args: + ag (object): The Agave job object used to interact with the job. + job_id (str): The unique identifier of the job to monitor. + time_lapse (int, optional): Time interval, in seconds, to wait between status + checks. Defaults to 15 seconds. + + Returns: + str: The final status of the job. Typical values include "FINISHED", "FAILED", + and "STOPPED". + + Raises: + No exceptions are explicitly raised, but potential exceptions raised by the Agave + job object or other called functions/methods will propagate. + """ + + previous_status = None + # Initially check if the job is already running + status = ag.jobs.getStatus(jobId=job_id)["status"] + + job_details = ag.jobs.get(jobId=job_id) + max_hours = job_details["maxHours"] + + # Using tqdm to provide visual feedback while waiting for job to start + with tqdm(desc="Waiting for job to start", dynamic_ncols=True) as pbar: + while status not in ["RUNNING", "FINISHED", "FAILED", "STOPPED"]: + time.sleep(time_lapse) + status = ag.jobs.getStatus(jobId=job_id)["status"] + pbar.update(1) + pbar.set_postfix_str(f"Status: {status}") + + # Once the job is running, monitor it for up to maxHours + max_iterations = int(max_hours * 3600 // time_lapse) + + # Using tqdm for progress bar + for _ in tqdm(range(max_iterations), desc="Monitoring job", ncols=100): + status = ag.jobs.getStatus(jobId=job_id)["status"] + + # Print status if it has changed + if status != previous_status: + tqdm.write(f"\tStatus: {status}") + previous_status = status + + # Break the loop if job reaches one of these statuses + if status in ["FINISHED", "FAILED", "STOPPED"]: + break + + time.sleep(time_lapse) + else: + # This block will execute if the for loop completes without a 'break' + print("Warning: Maximum monitoring time reached!") + + return status \ No newline at end of file diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..09b329c --- /dev/null +++ b/poetry.lock @@ -0,0 +1,474 @@ +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + +[[package]] +name = "agavepy" +version = "0.9.5" +description = "SDK for Tapis" +optional = false +python-versions = "*" +files = [ + {file = "agavepy-0.9.5-py2.py3-none-any.whl", hash = "sha256:6d80f5cd8601ece9ca8c9eb6cbce58b7f28a1dbfc4037c59c87137aa18928cb4"}, + {file = "agavepy-0.9.5.tar.gz", hash = "sha256:a0e62e6aacbf95618da4c5574a2cd3ee14545435331aee000162b4882085eec4"}, +] + +[package.dependencies] +"backports.ssl-match-hostname" = ">=3.4.0.2" +cloudpickle = ">=0.4.0" +configparser = ">=3.5.0" +future = ">=0.16.0" +Jinja2 = ">=2.7.3" +py = ">=1.4.26" +pytest = ">=2.7.0" +python-dateutil = ">=2.4.2" +requests = ">=2.6.0" +requests-toolbelt = ">=0.7.1" +six = ">=1.9.0" +websocket-client = "0.53.0" + +[[package]] +name = "backports-ssl-match-hostname" +version = "3.7.0.1" +description = "The ssl.match_hostname() function from Python 3.5" +optional = false +python-versions = "*" +files = [ + {file = "backports.ssl_match_hostname-3.7.0.1.tar.gz", hash = "sha256:bb82e60f9fbf4c080eabd957c39f0641f0fc247d9a16e31e26d594d8f42b9fd2"}, +] + +[[package]] +name = "certifi" +version = "2023.7.22" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.6" +files = [ + {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, + {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.3.0" +description = "The Real First Universal Charset Detector. 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"^4.66.1" +agavepy = "^0.9.5" + + +[tool.poetry.group.dev.dependencies] +pytest = "^7.4.2" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" \ No newline at end of file diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_jobs.py b/tests/test_jobs.py new file mode 100644 index 0000000..f31041e --- /dev/null +++ b/tests/test_jobs.py @@ -0,0 +1,37 @@ +import time +import unittest +from unittest.mock import Mock, patch +import dsjobs as ds + +class TestGetStatus(unittest.TestCase): + + @patch('time.sleep', Mock()) # Mocks the sleep function + def test_get_status(self): + # Mock the Agave job object + mock_agave = Mock() + + # Define behavior for getStatus method + mock_agave.jobs.getStatus.side_effect = [ + {"status": "PENDING"}, + {"status": "PENDING"}, + {"status": "RUNNING"}, + {"status": "RUNNING"}, + {"status": "FINISHED"} + ] + + # Define behavior for get method + mock_agave.jobs.get.return_value = {"maxHours": 0.01} # Equivalent to 36 seconds + + # Call get_status + status = ds.get_status(mock_agave, "some_job_id", time_lapse=1) + + # Assert that the final status is "FINISHED" + self.assertEqual(status, "FINISHED") + + # Assert the methods were called the expected number of times + mock_agave.jobs.getStatus.assert_called_with(jobId="some_job_id") + self.assertEqual(mock_agave.jobs.getStatus.call_count, 5) + mock_agave.jobs.get.assert_called_once_with(jobId="some_job_id") + +if __name__ == "__main__": + unittest.main()