first commit

.gitignore

@@ -0,0 +1,162 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+*.log
+# 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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/

Dockerfile

@@ -0,0 +1,4 @@
+FROM docker.io/library/python:3.9
+
+RUN pip install cwl-utils==0.14 attrs loguru 
+

README.md

@@ -1,2 +1,12 @@
 # zoo-argowf-runner
+
 Zoo runner using Argo Workflows
+
+## Environment variables
+
+STORAGE_CLASS
+DEFAULT_VOLUME_SIZE
+DEFAULT_MAX_CORES
+DEFAULT_MAX_RAM
+ARGO_WF_ENDPOINT
+ARGO_WF_TOKEN 

pyproject.toml

@@ -0,0 +1,28 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "zoo-argowf-runner"
+description = "Zoo runner using Argo Workflows to process an Application Package encoded in CWL."
+dynamic = ["version"]
+readme = "README.md"
+requires-python = ">=3.8"
+
+dependencies = []
+
+
+[tool.hatch.version]
+path = "zoo_argowf_runner/__about__.py"
+
+[tool.hatch.envs.default]
+dependencies = [
+    "PyYAML",
+    "hera",
+    "cwl-utils",
+    "click",
+    "cwl-utils==0.14",
+    "attrs",
+    "loguru",
+
+]

tests/tests_water_bodies.py

@@ -0,0 +1,65 @@
+import os
+import unittest
+
+from tests.water_bodies.service import water_bodies
+
+
+class TestWaterBodiesService(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        class ZooStub(object):
+            def __init__(self):
+                self.SERVICE_SUCCEEDED = 3
+                self.SERVICE_FAILED = 4
+
+            def update_status(self, conf, progress):
+                print(f"Status {progress}")
+
+            def _(self, message):
+                print(f"invoked _ with {message}")
+
+        try:
+            import zoo
+        except ImportError:
+            print("Not running in zoo instance")
+
+            zoo = ZooStub()
+
+        os.environ["ARGO_WF_ENDPOINT"] = "http://localhost:2746"
+        os.environ["ARGO_WF_TOKEN"] = (
+            ""
+        )
+        os.environ["ARGO_WF_SYNCHRONIZATION_CM"] = "semaphore-water-bodies"
+
+        cls.zoo = zoo
+
+        conf = {}
+        conf["lenv"] = {"message": ""}
+        conf["lenv"] = {"Identifier": "water-bodies", "usid": "1234"}
+        conf["tmpPath"] = "/tmp"
+        conf["main"] = {"tmpUrl": "http://localhost/logs/", "namespace": "ns1"}
+        cls.conf = conf
+
+        inputs = {
+            "aoi": {"value": "-121.399,39.834,-120.74,40.472"},
+            "bands": {"value": ["green", "nir"]},
+            "epsg": {"value": "EPSG:4326"},
+            "stac_items": {
+                "value": [
+                    "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a/items/S2A_10TFK_20210708_0_L2A",  # noqa
+                ]
+            },
+        }
+
+        cls.inputs = inputs
+
+        outputs = {"Result": {"value": ""}}
+
+        cls.outputs = outputs
+
+    def test_execution(self):
+        exit_code = water_bodies(
+            conf=self.conf, inputs=self.inputs, outputs=self.outputs
+        )
+
+        self.assertEqual(exit_code, self.zoo.SERVICE_SUCCEEDED)