diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 71710a6..cfa6f9e 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -39,7 +39,16 @@ "redhat.vscode-yaml", "ryanluker.vscode-coverage-gutters", "charliermarsh.ruff", - "ms-azuretools.vscode-docker" + "ms-azuretools.vscode-docker", + "ms-python.debugpy", + "ms-python.vscode-python-envs", + "ms-python.vscode-pylance", + "ms-toolsai.vscode-jupyter-slideshow", + "ms-toolsai.vscode-jupyter-cell-tags", + "ms-toolsai.jupyter-renderers", + "ms-toolsai.jupyter", + "ms-azuretools.vscode-containers", + "ms-toolsai.jupyter-keymap" ] } }, diff --git a/README.md b/README.md index fee2dff..0c5acd2 100644 --- a/README.md +++ b/README.md @@ -31,3 +31,24 @@ Or if it is a commandline tool then you might put some example commands here: ``` python -m python_interface_to_workflows --version ``` + +# Using Copier +```bash +mkdir new_directory_path +cd new_directory_path +git init +git remote add origin {origin ssh} +git branch -M main + +cd .. +``` +then either: +```bash +git clone git@github.com:DiamondLightSource/python-interface-to-workflows.git +copier copy {this_repo's_path} {new_directory_path} +``` +or: +```bash +copier copy git@github.com:DiamondLightSource/python-copier-template.git new directory path +``` +rebuild in dev container without cache diff --git a/scripts/lintyaml.sh b/scripts/lintyaml.sh index 3de474e..9ebc381 100644 --- a/scripts/lintyaml.sh +++ b/scripts/lintyaml.sh @@ -1,6 +1,6 @@ #!/bin/bash cd src/python_interface_to_workflows/templates -for file in * +for file in *.yaml; do argo lint "$file" --offline SUCCESSFULLINT=$? diff --git a/scripts/makecopiercorrect.sh b/scripts/makecopiercorrect.sh index 0f2a966..cdc2221 100644 --- a/scripts/makecopiercorrect.sh +++ b/scripts/makecopiercorrect.sh @@ -6,17 +6,56 @@ cp ../templates/*example*.txt "../../copier_template/src/{{ project_name }}/temp for file in "../../copier_template/src/{{ project_name }}/workflow_definitions"/* do + [[ -d "$file" ]] && continue [[ $file == *.jinja ]] && continue + sed -i 's/python-interface-to-workflows/{{repo_name}}/g' "$file" sed -i 's/DiamondLightSource/{{github_org}}/g' "$file" + + sed -i '1i{% raw %}' "$file" + echo '{% endraw %}' >> "$file" + + sed -i \ + -e 's/{{repo_name}}/{% endraw %}{{repo_name}}{% raw %}/g' \ + -e 's/{{github_org}}/{% endraw %}{{github_org}}{% raw %}/g' \ + "$file" + mv "$file" "$file.jinja" done +for file in "../../copier_template/src/{{ project_name }}/workflow_definitions/notebooks"/* +do + [[ -d "$file" ]] && continue + [[ $file == *.jinja ]] && continue + + sed -i 's/python-interface-to-workflows/{{repo_name}}/g' "$file" + sed -i 's/DiamondLightSource/{{github_org}}/g' "$file" + sed -i '1i{% raw %}' "$file" + echo '{% endraw %}' >> "$file" + + sed -i \ + -e 's/{{repo_name}}/{% endraw %}{{repo_name}}{% raw %}/g' \ + -e 's/{{github_org}}/{% endraw %}{{github_org}}{% raw %}/g' \ + "$file" + + mv "$file" "$file.jinja" +done for file in "../../copier_template/src/{{ project_name }}/templates"/* do + [[ -d "$file" ]] && continue [[ $file == *.jinja ]] && continue + sed -i 's/python-interface-to-workflows/{{repo_name}}/g' "$file" sed -i 's/DiamondLightSource/{{github_org}}/g' "$file" + + sed -i '1i{% raw %}' "$file" + echo '{% endraw %}' >> "$file" + + sed -i \ + -e 's/{{repo_name}}/{% endraw %}{{repo_name}}{% raw %}/g' \ + -e 's/{{github_org}}/{% endraw %}{{github_org}}{% raw %}/g' \ + "$file" + mv "$file" "$file.jinja" done git add "../../copier_template/src/{{ project_name }}/workflow_definitions"/* diff --git a/scripts/runthefiles.sh b/scripts/runthefiles.sh index a7453b4..960a7d8 100644 --- a/scripts/runthefiles.sh +++ b/scripts/runthefiles.sh @@ -5,4 +5,5 @@ do uv run "$file" done mv *.yaml ../templates/ +mv *.txt ../templates/ git add -u ../templates/ diff --git a/src/copier_template/.devcontainer/devcontainer.json b/src/copier_template/.devcontainer/devcontainer.json index 71710a6..cfa6f9e 100644 --- a/src/copier_template/.devcontainer/devcontainer.json +++ b/src/copier_template/.devcontainer/devcontainer.json @@ -39,7 +39,16 @@ "redhat.vscode-yaml", "ryanluker.vscode-coverage-gutters", "charliermarsh.ruff", - "ms-azuretools.vscode-docker" + "ms-azuretools.vscode-docker", + "ms-python.debugpy", + "ms-python.vscode-python-envs", + "ms-python.vscode-pylance", + "ms-toolsai.vscode-jupyter-slideshow", + "ms-toolsai.vscode-jupyter-cell-tags", + "ms-toolsai.jupyter-renderers", + "ms-toolsai.jupyter", + "ms-azuretools.vscode-containers", + "ms-toolsai.jupyter-keymap" ] } }, diff --git a/src/copier_template/pyproject.toml.jinja b/src/copier_template/pyproject.toml.jinja index cad7d38..9eec731 100644 --- a/src/copier_template/pyproject.toml.jinja +++ b/src/copier_template/pyproject.toml.jinja @@ -68,7 +68,6 @@ reportMissingImports = false # Ignore missing stubs in imported modules reportMissingTypeStubs = "none" reportMissingModuleSource="warning" reportInvalidTypeForm="warning" -reportMissingImports="warning" reportUndefinedVariable="warning" reportAbstractUsage="warning" reportArgumentType="warning" diff --git a/src/copier_template/scripts/lintyaml.sh.jinja b/src/copier_template/scripts/lintyaml.sh.jinja index 7b0b6e8..5c984df 100644 --- a/src/copier_template/scripts/lintyaml.sh.jinja +++ b/src/copier_template/scripts/lintyaml.sh.jinja @@ -1,6 +1,6 @@ #!/bin/bash cd src/{{project_name}}/templates -for file in * +for file in *.yaml; do argo lint "$file" --offline SUCCESSFULLINT=$? diff --git a/src/copier_template/scripts/runthefiles.sh.jinja b/src/copier_template/scripts/runthefiles.sh.jinja index ca0bea2..f324322 100644 --- a/src/copier_template/scripts/runthefiles.sh.jinja +++ b/src/copier_template/scripts/runthefiles.sh.jinja @@ -5,4 +5,5 @@ do uv run "$file" done mv *.yaml ../templates/ +mv *.txt ../templates/ git add -u ../templates/ diff --git a/src/copier_template/src/README.md.jinja b/src/copier_template/src/README.md.jinja index 00f1d90..6725840 100644 --- a/src/copier_template/src/README.md.jinja +++ b/src/copier_template/src/README.md.jinja @@ -4,7 +4,8 @@ HOST=https://argo-workflows.workflows.diamond.ac.uk/ (to submit to the production cluster) DEFAULT_IMAGE= (usually python 3.10) -NAMESPACE= (the cluster you wish to run the templates on) +VISIT= (the VISIT you wish to run the templates on) +EXPIRY= 3. Build the dev container diff --git a/src/copier_template/src/{{ project_name }}/auth/keycloak_checker.py.jinja b/src/copier_template/src/{{ project_name }}/auth/keycloak_checker.py.jinja index 04dd688..2607840 100644 --- a/src/copier_template/src/{{ project_name }}/auth/keycloak_checker.py.jinja +++ b/src/copier_template/src/{{ project_name }}/auth/keycloak_checker.py.jinja @@ -9,12 +9,12 @@ from {{project_name}}.auth.open_auth_url import open_auth_url def set_token_env_variable() -> str: keycloak_openid = KeycloakOpenID( - client_id="workflows-dashboard", - server_url="https://identity.diamond.ac.uk/", - realm_name="dls", - client_secret_key="", - pool_maxsize=1, - ) + client_id="workflows-cli", + server_url="https://identity.diamond.ac.uk/", + realm_name="dls", + client_secret_key="", + pool_maxsize=1, + ) port = 8000 code_verifier = generate_code_verifier() code_challenge, code_challenge_method = generate_code_challenge(code_verifier) @@ -25,14 +25,26 @@ def set_token_env_variable() -> str: code_challenge=code_challenge, code_challenge_method=code_challenge_method, ) - open_auth_url(auth_url) - token: dict[str, str] = ( # pyright: ignore[reportUnknownVariableType] - keycloak_openid.token( # pyright: ignore[reportUnknownMemberType] - grant_type="authorization_code", - code=os.environ["AUTH"], - redirect_uri=f"http://localhost:{port}/", - code_verifier=code_verifier, - ) + match open_auth_url(auth_url, port): + case True: + token: dict[str, str] = ( # pyright: ignore[reportUnknownVariableType] + keycloak_openid.token( # pyright: ignore[reportUnknownMemberType] + grant_type="authorization_code", + code=os.environ.get("AUTH"), # pyright: ignore + redirect_uri=f"http://localhost:{port}/", + code_verifier=code_verifier, + ) + ) + case False: + token: dict[str, str] = keycloak_openid.refresh_token( # pyright: ignore + str(os.environ.get("REFRESHTOKEN")) # pyright: ignore + ) + token_info: dict[str, int | str | dict[str, list[str]]] = ( # pyright: ignore + keycloak_openid.decode_token(token["access_token"]) # pyright: ignore ) + expire_time = int(token_info["exp"]) + 1500 # pyright: ignore + dotenv.set_key("src/.env", "EXPIRY", str(expire_time).strip("'")) dotenv.set_key("src/.env", "TOKEN", token["access_token"].strip("'")) + dotenv.set_key("src/.env", "REFRESHTOKEN", token["refresh_token"].strip("'")) + dotenv.load_dotenv(dotenv_path="src/.env", override=True) return token["access_token"] # pyright: ignore[reportUnknownArgumentType] diff --git a/src/copier_template/src/{{ project_name }}/auth/open_auth_url.py b/src/copier_template/src/{{ project_name }}/auth/open_auth_url.py index 5a18266..9acae95 100644 --- a/src/copier_template/src/{{ project_name }}/auth/open_auth_url.py +++ b/src/copier_template/src/{{ project_name }}/auth/open_auth_url.py @@ -1,10 +1,13 @@ import os import socket +import time import urllib.parse import webbrowser from http.server import BaseHTTPRequestHandler, HTTPServer from typing import cast +import dotenv + class _ReusingHTTPServer(HTTPServer): allow_reuse_address = True @@ -26,16 +29,23 @@ def do_GET(self): self.wfile.write(b"Missing authorization code.") -def open_auth_url(auth_url: str) -> None: - httpd = _ReusingHTTPServer(("localhost", 8000), CallbackHandler) - webbrowser.open(auth_url) - try: - httpd.handle_request() - os.environ["AUTH"] = httpd.auth_code - except OSError: - os.environ["AUTH"] = "" - print("ERROR: Port in use. Please restart your terminal.") - exit(1) - finally: - httpd.socket.shutdown(socket.SHUT_RDWR) - httpd.server_close() +def open_auth_url(auth_url: str, port: int) -> bool: + dotenv.load_dotenv(dotenv_path="src/.env", override=True) + expiry_str: str = os.environ.get("EXPIRY").strip("'") # pyright: ignore + if (expiry_str == "" or int(expiry_str)) <= float(time.time()): + httpd = _ReusingHTTPServer(("localhost", port), CallbackHandler) + webbrowser.open(auth_url) + try: + httpd.handle_request() + os.environ["AUTH"] = httpd.auth_code + dotenv.set_key("src/.env", "AUTH", httpd.auth_code) + except OSError: + os.environ["AUTH"] = "" + print("ERROR: Port in use. Please restart your terminal.") + exit(1) + finally: + httpd.socket.shutdown(socket.SHUT_RDWR) + httpd.server_close() + return True + else: + return False diff --git a/src/copier_template/src/{{ project_name }}/submit_to_argo.py.jinja b/src/copier_template/src/{{ project_name }}/submit_to_argo.py.jinja index f0e49e4..1b30683 100644 --- a/src/copier_template/src/{{ project_name }}/submit_to_argo.py.jinja +++ b/src/copier_template/src/{{ project_name }}/submit_to_argo.py.jinja @@ -12,7 +12,7 @@ from {{project_name}}.auth.keycloak_checker import set_token_env_variable def submit_workflow_to_argo(w: Workflow): set_token_env_variable() dotenv.load_dotenv(dotenv_path="src/.env", override=True) - w.namespace = os.environ.get("NAMESPACE") + w.namespace = os.environ.get("VISIT") w.workflows_service = WorkflowsService( host=str(os.environ.get("HOST")).strip("'"), token=str(os.environ.get("TOKEN")).strip("'"), diff --git a/src/copier_template/src/{{ project_name }}/templates/example.txt.jinja b/src/copier_template/src/{{ project_name }}/templates/example.txt.jinja index 736759b..3e74853 100644 --- a/src/copier_template/src/{{ project_name }}/templates/example.txt.jinja +++ b/src/copier_template/src/{{ project_name }}/templates/example.txt.jinja @@ -1,3 +1,4 @@ +{% raw %} apiVersion: argoproj.io/v1alpha1 kind: Workflow metadata: @@ -7,7 +8,7 @@ metadata: Replicates the functionality of example.yaml workflows.argoproj.io/title: example remade via hera - workflows.diamond.ac.uk/repository: https://github.com/{{github_org}}/{{repo_name}} + workflows.diamond.ac.uk/repository: https://github.com/{% endraw %}{{github_org}}{% raw %}/{% endraw %}{{repo_name}}{% raw %} labels: workflows.diamond.ac.uk/science-group-examples: 'true' spec: @@ -212,3 +213,4 @@ spec: resources: requests: storage: 1Gi +{% endraw %} diff --git a/src/copier_template/src/{{ project_name }}/workflow_definitions/create_example_template.py.jinja b/src/copier_template/src/{{ project_name }}/workflow_definitions/create_example_template.py.jinja index 6a6aa90..65be398 100644 --- a/src/copier_template/src/{{ project_name }}/workflow_definitions/create_example_template.py.jinja +++ b/src/copier_template/src/{{ project_name }}/workflow_definitions/create_example_template.py.jinja @@ -1,3 +1,4 @@ +{% raw %} from hera.workflows import ( DAG, Artifact, @@ -153,7 +154,7 @@ with Workflow( "workflows.argoproj.io/title": "example remade via hera", "workflows.argoproj.io/description": """Replicates the functionality of example.yaml""", - "workflows.diamond.ac.uk/repository": "https://github.com/{{github_org}}/{{repo_name}}", + "workflows.diamond.ac.uk/repository": "https://github.com/{% endraw %}{{github_org}}{% raw %}/{% endraw %}{{repo_name}}{% raw %}", }, volumes=Volume(name="tmpdir", mount_path="/tmp/", size="1Gi"), ) as w: @@ -178,5 +179,6 @@ example.yaml""", [install, params] >> makeimages >> makehdf5 # pyright: ignore -with open("example.yaml", "w") as div: +with open("example.txt", "w") as div: div.write(w.to_yaml()) # pyright: ignore[reportUnknownMemberType] +{% endraw %} diff --git a/src/copier_template/src/{{ project_name }}/workflow_definitions/notebooks/notebook_division.ipynb.jinja b/src/copier_template/src/{{ project_name }}/workflow_definitions/notebooks/notebook_division.ipynb.jinja new file mode 100644 index 0000000..51071cc --- /dev/null +++ b/src/copier_template/src/{{ project_name }}/workflow_definitions/notebooks/notebook_division.ipynb.jinja @@ -0,0 +1,116 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "1e3146f1", + "metadata": {}, + "source": [ + "# Running in VSCode:\n", + "\n", + "1. Set kernal to python-interface-to-workflows 3.11.x\n", + "2. Hit F1, run Jupyter: Import Notebook to Script\n", + "3. Click notebook_division.ipynb\n", + "4. Run the cells sequentially" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "494174ef", + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "\n", + "from hera.workflows import (\n", + " Artifact,\n", + " EmptyDirVolume,\n", + " Steps,\n", + " Workflow,\n", + " script, # pyright: ignore[reportUnknownVariableType]\n", + ")\n", + "from hera.workflows import models as m\n", + "\n", + "\n", + "@script(\n", + " volume_mounts=[m.VolumeMount(name=\"output-dir\", mount_path=\"/output-dir/\")],\n", + " outputs=Artifact(name=\"json-output\", path=\"/output-dir/output.json\"),\n", + ")\n", + "def do_division(a: int, b: int):\n", + " div = a / b\n", + " intdiv = a // b\n", + " remain = a % b\n", + " dictionary_of_results = {\n", + " \"divide\": div,\n", + " \"quotient\": intdiv,\n", + " \"remainder\": remain,\n", + " }\n", + " with open(\"/output-dir/output.json\", \"w\") as otpt:\n", + " json.dump(dictionary_of_results, otpt)\n", + "\n", + "\n", + "with Workflow(\n", + " generate_name=\"hera-division-\", # when running on graphql this should be name\n", + " entrypoint=\"divide\",\n", + " api_version=\"argoproj.io/v1alpha1\",\n", + " kind=\"Workflow\", # ClusterWorkflowTemplate\", when on graphql\n", + " labels={\"workflows.diamond.ac.uk/science-group-examples\": \"true\"},\n", + " annotations={\n", + " \"workflows.argoproj.io/title\": \"Division via hera test\",\n", + " \"workflows.argoproj.io/description\": \"\"\"Takes a numerical input and returns\n", + " the remainder, output float, and output string to a json file\"\"\",\n", + " \"workflows.diamond.ac.uk/repository\": \"https://github.com/DiamondLightSource/python-interface-to-workflows\",\n", + " },\n", + " volumes=EmptyDirVolume(name=\"output-dir\", mount_path=\"/output-dir\"),\n", + ") as w:\n", + " with Steps(name=\"divide\"):\n", + " do_division(name=\"first\", arguments={\"a\": 2, \"b\": 5})\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "04708f46", + "metadata": {}, + "outputs": [], + "source": [ + "with open(\"division_from_jupyter.yaml\", \"w\") as div:\n", + " div.write(w.to_yaml()) # pyright: ignore[reportUnknownMemberType]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7e9f88cb", + "metadata": {}, + "outputs": [], + "source": [ + "from {{project_name}}.submit_to_argo import submit_workflow_to_argo\n", + "\n", + "submit_workflow_to_argo(w)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "python-interface-to-workflows (3.11.x)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.15" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/src/copier_template/src/{{ project_name }}/workflow_definitions/notebooks/notebook_example.ipynb.jinja b/src/copier_template/src/{{ project_name }}/workflow_definitions/notebooks/notebook_example.ipynb.jinja new file mode 100644 index 0000000..aca499c --- /dev/null +++ b/src/copier_template/src/{{ project_name }}/workflow_definitions/notebooks/notebook_example.ipynb.jinja @@ -0,0 +1,251 @@ +{% raw %}{ + "cells": [ + { + "cell_type": "markdown", + "id": "1e3146f1", + "metadata": {}, + "source": [ + "# Running in VSCode:\n", + "\n", + "1. Set kernal to python-interface-to-workflows 3.11.x\n", + "2. Hit F1, run Jupyter: Import Notebook to Script\n", + "3. Click notebook_example.ipynb\n", + "4. Run the cells sequentially" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "494174ef", + "metadata": {}, + "outputs": [], + "source": [ + "from hera.workflows import (\n", + " DAG,\n", + " Artifact,\n", + " Parameter,\n", + " Volume,\n", + " Workflow,\n", + " script, # pyright: ignore[reportUnknownVariableType]\n", + ")\n", + "from hera.workflows import models as m\n", + "from hera.workflows.archive import NoneArchiveStrategy\n", + "\n", + "\n", + "@script(\n", + " command=[\"python\"],\n", + " volume_mounts=[m.VolumeMount(name=\"tmpdir\", mount_path=\"/tmp\")],\n", + ")\n", + "def install_dependencies():\n", + " import subprocess\n", + "\n", + " print(\"creating venv\")\n", + "\n", + " subprocess.check_call([\"python\", \"-m\", \"venv\", \"/tmp/venv\"])\n", + " subprocess.check_call(\n", + " [\"/tmp/venv/bin/pip\", \"install\", \"pillow\", \"h5py\", \"numpy\", \"hera\"]\n", + " )\n", + "\n", + "\n", + "@script(\n", + " command=[\"python\"],\n", + " outputs=Parameter(\n", + " name=\"out-parameters\", value_from=m.ValueFrom(path=\"/tmp/parameters.json\")\n", + " ),\n", + " volume_mounts=[m.VolumeMount(name=\"tmpdir\", mount_path=\"/tmp\")],\n", + ")\n", + "def generate_parameters(\n", + " png: str,\n", + " jpg: str,\n", + " jpeg: str,\n", + " tif: str,\n", + " tiff: str,\n", + "):\n", + " import json\n", + "\n", + " params: list[dict[str, int | list[int] | str] | None] = [\n", + " {\"width\": 500, \"height\": 500, \"weights\": [255, 1, 100], \"extension\": \"png\"}\n", + " if png.lower() == \"true\"\n", + " else None,\n", + " {\"width\": 600, \"height\": 200, \"weights\": [100, 150, 100], \"extension\": \"jpg\"}\n", + " if jpg.lower() == \"true\"\n", + " else None,\n", + " {\"width\": 300, \"height\": 400, \"weights\": [100, 150, 100], \"extension\": \"jpeg\"}\n", + " if jpeg.lower() == \"true\"\n", + " else None,\n", + " {\"width\": 300, \"height\": 200, \"weights\": [230, 100, 1], \"extension\": \"tif\"}\n", + " if tif.lower() == \"true\"\n", + " else None,\n", + " {\"width\": 200, \"height\": 300, \"weights\": [230, 100, 1], \"extension\": \"tiff\"}\n", + " if tiff.lower() == \"true\"\n", + " else None,\n", + " ]\n", + " params_to_write: list[dict[str, int | list[int] | str]] = [\n", + " image_params for image_params in params if image_params is not None\n", + " ]\n", + " with open(\"/tmp/parameters.json\", \"w\") as f:\n", + " json.dump(params_to_write, f)\n", + "\n", + "\n", + "@script(\n", + " command=[\"/tmp/venv/bin/python\"],\n", + " volume_mounts=[m.VolumeMount(name=\"tmpdir\", mount_path=\"/tmp\")],\n", + " outputs=[\n", + " Parameter(\n", + " name=\"out-paths\",\n", + " value_from=m.ValueFrom(\n", + " path=\"/tmp/{{inputs.parameters.extension}}-path.json\"\n", + " ),\n", + " ),\n", + " Artifact(\n", + " name=\"{{inputs.parameters.extension}}-image\",\n", + " path=\"/tmp/{{inputs.parameters.extension}}-image.{{inputs.parameters.extension}}\",\n", + " archive=NoneArchiveStrategy(),\n", + " ),\n", + " ],\n", + ")\n", + "def create_image(\n", + " width: int, height: int, weights: tuple[int, int, int], extension: str\n", + "):\n", + " import json\n", + "\n", + " from PIL import Image\n", + "\n", + " def create_pattern(\n", + " width: int,\n", + " height: int,\n", + " weights: tuple[int, int, int],\n", + " ) -> Image.Image:\n", + " print(f\"width: {width}\")\n", + " print(f\"height: {height}\")\n", + " print(f\"RBG weights: {weights}\")\n", + " image = Image.new(\"RGB\", (width, height))\n", + " pixels = image.load()\n", + " for i in range(width):\n", + " for j in range(height):\n", + " pixels[i, j] = ( # pyright: ignore[reportOptionalSubscript]\n", + " (i + j * 50) % weights[0],\n", + " weights[1],\n", + " (i * 300 + j) % weights[2],\n", + " )\n", + " return image\n", + "\n", + " image = create_pattern(width, height, weights)\n", + " path = f\"/tmp/{extension}-image.{extension}\"\n", + " image.save(path)\n", + " with open(f\"/tmp/{extension}-path.json\", \"w\") as f:\n", + " json.dump(path, f)\n", + "\n", + "\n", + "@script(\n", + " command=[\"/tmp/venv/bin/python\"],\n", + " volume_mounts=[m.VolumeMount(name=\"tmpdir\", mount_path=\"/tmp\")],\n", + " outputs=Artifact(\n", + " name=\"hdf5output\",\n", + " path=\"/tmp/images.hdf5\",\n", + " archive=NoneArchiveStrategy(),\n", + " ),\n", + ")\n", + "def to_hdf5(paths: str):\n", + "\n", + " import h5py # pyright: ignore[reportMissingTypeStubs]\n", + " import numpy as np\n", + " from PIL import Image\n", + "\n", + " print(\"creating hdf5 file\")\n", + " with h5py.File(\"/tmp/images.hdf5\", \"w\") as f:\n", + " for i, path in enumerate(paths):\n", + " path = path.strip('\"')\n", + " print(f\"Got {path}\")\n", + " with Image.open(path) as image:\n", + " arr = np.array(image)\n", + " f.create_dataset( # pyright: ignore[reportUnknownMemberType]\n", + " f\"image_{i}\", data=arr, dtype=arr.dtype\n", + " )\n", + " print(\"done\")\n", + "\n", + "\n", + "with Workflow(\n", + " generate_name=\"hera-example-\", # when running on graphql this should be name\n", + " entrypoint=\"workflowentry\",\n", + " api_version=\"argoproj.io/v1alpha1\",\n", + " kind=\"Workflow\", # ClusterWorkflowTemplate\", when on graphql\n", + " labels={\"workflows.diamond.ac.uk/science-group-examples\": \"true\"},\n", + " annotations={\n", + " \"workflows.argoproj.io/title\": \"example remade via hera\",\n", + " \"workflows.argoproj.io/description\": \"\"\"Replicates the functionality of\n", + "example.yaml\"\"\",\n", + " \"workflows.diamond.ac.uk/repository\": \"https://github.com/DiamondLightSource/python-interface-to-workflows\",\n", + " },\n", + " volumes=Volume(name=\"tmpdir\", mount_path=\"/tmp/\", size=\"1Gi\"),\n", + ") as w:\n", + " with DAG(name=\"workflowentry\"):\n", + " install = install_dependencies(name=\"install\")\n", + " params = generate_parameters(\n", + " name=\"params\",\n", + " arguments={\n", + " \"png\": \"True\",\n", + " \"jpg\": \"True\",\n", + " \"jpeg\": \"True\",\n", + " \"tif\": \"True\",\n", + " \"tiff\": \"True\",\n", + " },\n", + " )\n", + " makeimages = create_image(with_param=params.get_parameter(\"out-parameters\"))\n", + " makehdf5 = to_hdf5(\n", + " arguments={\n", + " \"paths\": makeimages.get_parameter(\"out-paths\"),\n", + " }\n", + " )\n", + " [install, params] >> makeimages >> makehdf5 # pyright: ignore\n", + "\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "04708f46", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "with open(\"example.txt\", \"w\") as div:\n", + " div.write(w.to_yaml()) # pyright: ignore[reportUnknownMemberType]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7e9f88cb", + "metadata": {}, + "source": [ + "from {% endraw %}{{project_name}}{% raw %}.submit_to_argo import submit_workflow_to_argo\n", + "\n", + "submit_workflow_to_argo(w)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "python-interface-to-workflows (3.11.x)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.15" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} +{% endraw %} diff --git a/src/copier_template/tests/test_keycloak_checker.py.jinja b/src/copier_template/tests/test_keycloak_checker.py.jinja index 2eda176..322b17b 100644 --- a/src/copier_template/tests/test_keycloak_checker.py.jinja +++ b/src/copier_template/tests/test_keycloak_checker.py.jinja @@ -1,35 +1,75 @@ import os -from unittest.mock import MagicMock, patch +from unittest.mock import MagicMock, call, patch + +from pytest import mark from {{project_name}}.auth.keycloak_checker import set_token_env_variable +@mark.parametrize( + "staging,port,return_present", + [ + (True, 5173, True), + (False, 8000, False), + (True, 5173, False), + (False, 8000, True), + ], +) +@patch("{{project_name}}.auth.keycloak_checker.dotenv.load_dotenv") +@patch("{{project_name}}.auth.keycloak_checker.dotenv.set_key") @patch("{{project_name}}.auth.keycloak_checker.KeycloakOpenID") @patch("{{project_name}}.auth.keycloak_checker.generate_code_verifier") @patch("{{project_name}}.auth.keycloak_checker.generate_code_challenge") @patch("{{project_name}}.auth.keycloak_checker.open_auth_url") -def test_return_key( +def test_set_token_env_variable( mock_open_auth_url: MagicMock, mock_gen_code_challenge: MagicMock, mock_gen_code_verifier: MagicMock, mock_gen_keycloak_id: MagicMock, + mock_set_key: MagicMock, + mock_load_env: MagicMock, + staging: bool, + port: int, + return_present: bool, ): mock_gen_code_verifier.return_value = "verifier" mock_gen_code_challenge.return_value = ("challenge", "S256") os.environ["AUTH"] = "auth_url_code" + os.environ["REFRESHTOKEN"] = "refresh" + keycloak = MagicMock() mock_gen_keycloak_id.return_value = keycloak - + mock_open_auth_url.return_value = return_present keycloak.auth_url.return_value = "https://mock.site" - keycloak.token.return_value = { + token = { "access_token": "fake_token", "refresh_token": "fake_refresh", } - assert set_token_env_variable() == "fake_token" - mock_open_auth_url.assert_called_once_with("https://mock.site", 8000) - keycloak.token.assert_called_once_with( - grant_type="authorization_code", - code="auth_url_code", - redirect_uri="http://localhost:8000/", - code_verifier="verifier", + keycloak.token.return_value = token + keycloak.refresh_token.return_value = token + keycloak.decode_token.return_value = {"exp": 123456789} + assert set_token_env_variable(staging) == "fake_token" + + mock_open_auth_url.assert_called_once_with("https://mock.site", port) + if return_present: + keycloak.token.assert_called_once_with( + grant_type="authorization_code", + code="auth_url_code", + redirect_uri=f"http://localhost:{port}/", + code_verifier="verifier", + ) + keycloak.refresh_token.assert_not_called() + else: + keycloak.refresh_token.assert_called_once_with("refresh") + keycloak.token.assert_not_called() + mock_set_key.assert_has_calls( + [ + call("src/.env", "EXPIRY", str(123456789 + 1500)), + call("src/.env", "TOKEN", "fake_token"), + call("src/.env", "REFRESHTOKEN", "fake_refresh"), + ] + ) + mock_load_env.assert_called_once_with( + dotenv_path="src/.env", + override=True, ) diff --git a/src/copier_template/tests/test_open_auth_url.py.jinja b/src/copier_template/tests/test_open_auth_url.py.jinja index f6d3393..bc3799a 100644 --- a/src/copier_template/tests/test_open_auth_url.py.jinja +++ b/src/copier_template/tests/test_open_auth_url.py.jinja @@ -7,22 +7,45 @@ from {{project_name}}.auth.open_auth_url import ( ) +@patch("{{project_name}}.auth.open_auth_url.dotenv.set_key") +@patch("{{project_name}}.auth.open_auth_url.dotenv.load_dotenv") +@patch("{{project_name}}.auth.open_auth_url.time.time") @patch("{{project_name}}.auth.open_auth_url.webbrowser.open") @patch("{{project_name}}.auth.open_auth_url._ReusingHTTPServer") def test_open_auth_url_normal_function( mock_http_server: MagicMock, mock_open_browser: MagicMock, + mock_time: MagicMock, + mock_load_env: MagicMock, + mock_set_key: MagicMock, ): + mock_time.return_value = 100 + os.environ["EXPIRY"] = "" + server = mock_http_server.return_value server.auth_code = "this_is_your_code" - open_auth_url("url") + + assert open_auth_url("url", 5173) is True + + mock_load_env.assert_called_once_with( + dotenv_path="src/.env", + override=True, + ) server.handle_request.assert_called_once() mock_open_browser.assert_called_once_with("url") + mock_set_key.assert_called_once_with( + "src/.env", + "AUTH", + "this_is_your_code", + ) server.socket.shutdown.assert_called_once() server.server_close.assert_called_once() assert os.environ["AUTH"] == "this_is_your_code" +@patch("{{project_name}}.auth.open_auth_url.dotenv.set_key") +@patch("{{project_name}}.auth.open_auth_url.dotenv.load_dotenv") +@patch("{{project_name}}.auth.open_auth_url.time.time") @patch("{{project_name}}.auth.open_auth_url.exit") @patch("{{project_name}}.auth.open_auth_url.webbrowser.open") @patch("{{project_name}}.auth.open_auth_url._ReusingHTTPServer") @@ -30,18 +53,48 @@ def test_open_auth_url_raises_error( mock_http_server: MagicMock, mock_open_browser: MagicMock, mock_exit: MagicMock, + mock_time: MagicMock, + mock_load_env: MagicMock, + mock_set_key: MagicMock, ): + mock_time.return_value = 100 + os.environ["EXPIRY"] = "" + server = mock_http_server.return_value - server.auth_code = "this_is_your_code" server.handle_request.side_effect = OSError - open_auth_url("url") + + assert open_auth_url("url", 5173) is True mock_open_browser.assert_called_once_with("url") + mock_load_env.assert_called_once() assert os.environ["AUTH"] == "" mock_exit.assert_called_once_with(1) + mock_set_key.assert_not_called() server.socket.shutdown.assert_called_once() server.server_close.assert_called_once() +@patch("{{project_name}}.auth.open_auth_url.webbrowser.open") +@patch("{{project_name}}.auth.open_auth_url.dotenv.load_dotenv") +@patch("{{project_name}}.auth.open_auth_url.time.time") +@patch("{{project_name}}.auth.open_auth_url._ReusingHTTPServer") +def test_open_auth_url_refresh_token( + mock_http_server: MagicMock, + mock_time: MagicMock, + mock_load_env: MagicMock, + mock_open_browser: MagicMock, +): + mock_time.return_value = 100 + os.environ["EXPIRY"] = "200" + assert open_auth_url("url", 5173) is False + + mock_load_env.assert_called_once_with( + dotenv_path="src/.env", + override=True, + ) + mock_http_server.assert_not_called() + mock_open_browser.assert_not_called() + + def test_handler_normal_function(): handler = CallbackHandler.__new__(CallbackHandler) handler.path = "/?code=this_is_your_code" diff --git a/src/python_interface_to_workflows/auth/keycloak_checker.py b/src/python_interface_to_workflows/auth/keycloak_checker.py index 71390fb..44e486e 100644 --- a/src/python_interface_to_workflows/auth/keycloak_checker.py +++ b/src/python_interface_to_workflows/auth/keycloak_checker.py @@ -36,14 +36,26 @@ def set_token_env_variable(staging: bool) -> str: code_challenge=code_challenge, code_challenge_method=code_challenge_method, ) - open_auth_url(auth_url, port) - token: dict[str, str] = ( # pyright: ignore[reportUnknownVariableType] - keycloak_openid.token( # pyright: ignore[reportUnknownMemberType] - grant_type="authorization_code", - code=os.environ["AUTH"], - redirect_uri=f"http://localhost:{port}/", - code_verifier=code_verifier, - ) + match open_auth_url(auth_url, port): + case True: + token: dict[str, str] = ( # pyright: ignore[reportUnknownVariableType] + keycloak_openid.token( # pyright: ignore[reportUnknownMemberType] + grant_type="authorization_code", + code=os.environ.get("AUTH"), # pyright: ignore + redirect_uri=f"http://localhost:{port}/", + code_verifier=code_verifier, + ) + ) + case False: + token: dict[str, str] = keycloak_openid.refresh_token( # pyright: ignore + str(os.environ.get("REFRESHTOKEN")) # pyright: ignore + ) + token_info: dict[str, int | str | dict[str, list[str]]] = ( # pyright: ignore + keycloak_openid.decode_token(token["access_token"]) # pyright: ignore ) + expire_time = int(token_info["exp"]) + 1500 # pyright: ignore + dotenv.set_key("src/.env", "EXPIRY", str(expire_time).strip("'")) dotenv.set_key("src/.env", "TOKEN", token["access_token"].strip("'")) + dotenv.set_key("src/.env", "REFRESHTOKEN", token["refresh_token"].strip("'")) + dotenv.load_dotenv(dotenv_path="src/.env", override=True) return token["access_token"] # pyright: ignore[reportUnknownArgumentType] diff --git a/src/python_interface_to_workflows/auth/open_auth_url.py b/src/python_interface_to_workflows/auth/open_auth_url.py index 2f0dcf9..9acae95 100644 --- a/src/python_interface_to_workflows/auth/open_auth_url.py +++ b/src/python_interface_to_workflows/auth/open_auth_url.py @@ -1,5 +1,6 @@ import os import socket +import time import urllib.parse import webbrowser from http.server import BaseHTTPRequestHandler, HTTPServer @@ -28,17 +29,23 @@ def do_GET(self): self.wfile.write(b"Missing authorization code.") -def open_auth_url(auth_url: str, port: int) -> None: - httpd = _ReusingHTTPServer(("localhost", port), CallbackHandler) - webbrowser.open(auth_url) - try: - httpd.handle_request() - os.environ["AUTH"] = httpd.auth_code - dotenv.set_key("src/.env", "AUTH", httpd.auth_code) - except OSError: - os.environ["AUTH"] = "" - print("ERROR: Port in use. Please restart your terminal.") - exit(1) - finally: - httpd.socket.shutdown(socket.SHUT_RDWR) - httpd.server_close() +def open_auth_url(auth_url: str, port: int) -> bool: + dotenv.load_dotenv(dotenv_path="src/.env", override=True) + expiry_str: str = os.environ.get("EXPIRY").strip("'") # pyright: ignore + if (expiry_str == "" or int(expiry_str)) <= float(time.time()): + httpd = _ReusingHTTPServer(("localhost", port), CallbackHandler) + webbrowser.open(auth_url) + try: + httpd.handle_request() + os.environ["AUTH"] = httpd.auth_code + dotenv.set_key("src/.env", "AUTH", httpd.auth_code) + except OSError: + os.environ["AUTH"] = "" + print("ERROR: Port in use. Please restart your terminal.") + exit(1) + finally: + httpd.socket.shutdown(socket.SHUT_RDWR) + httpd.server_close() + return True + else: + return False diff --git a/src/python_interface_to_workflows/submit_to_argo.py b/src/python_interface_to_workflows/submit_to_argo.py index 82b86db..0ec1233 100644 --- a/src/python_interface_to_workflows/submit_to_argo.py +++ b/src/python_interface_to_workflows/submit_to_argo.py @@ -12,7 +12,7 @@ def submit_workflow_to_argo(w: Workflow): set_token_env_variable(staging=True) dotenv.load_dotenv(dotenv_path="src/.env", override=True) - w.namespace = os.environ.get("NAMESPACE") + w.namespace = os.environ.get("VISIT") w.workflows_service = WorkflowsService( host=str(os.environ.get("HOST")).strip("'"), token=str(os.environ.get("TOKEN")).strip("'"), diff --git a/src/python_interface_to_workflows/templates/example.yaml b/src/python_interface_to_workflows/templates/example.txt similarity index 100% rename from src/python_interface_to_workflows/templates/example.yaml rename to src/python_interface_to_workflows/templates/example.txt diff --git a/src/python_interface_to_workflows/workflow_definitions/create_example_template.py b/src/python_interface_to_workflows/workflow_definitions/create_example_template.py index e718511..c8f4ce7 100644 --- a/src/python_interface_to_workflows/workflow_definitions/create_example_template.py +++ b/src/python_interface_to_workflows/workflow_definitions/create_example_template.py @@ -178,5 +178,5 @@ def to_hdf5(paths: str): [install, params] >> makeimages >> makehdf5 # pyright: ignore -with open("example.yaml", "w") as div: +with open("example.txt", "w") as div: div.write(w.to_yaml()) # pyright: ignore[reportUnknownMemberType] diff --git a/src/python_interface_to_workflows/workflow_definitions/notebooks/notebook_division.ipynb b/src/python_interface_to_workflows/workflow_definitions/notebooks/notebook_division.ipynb new file mode 100644 index 0000000..2e66d0d --- /dev/null +++ b/src/python_interface_to_workflows/workflow_definitions/notebooks/notebook_division.ipynb @@ -0,0 +1,116 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "1e3146f1", + "metadata": {}, + "source": [ + "# Running in VSCode:\n", + "\n", + "1. Set kernal to python-interface-to-workflows 3.11.x\n", + "2. Hit F1, run Jupyter: Import Notebook to Script\n", + "3. Click notebook_division.ipynb\n", + "4. Run the cells sequentially" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "494174ef", + "metadata": {}, + "outputs": [], + "source": [ + "import json\n", + "\n", + "from hera.workflows import (\n", + " Artifact,\n", + " EmptyDirVolume,\n", + " Steps,\n", + " Workflow,\n", + " script, # pyright: ignore[reportUnknownVariableType]\n", + ")\n", + "from hera.workflows import models as m\n", + "\n", + "\n", + "@script(\n", + " volume_mounts=[m.VolumeMount(name=\"output-dir\", mount_path=\"/output-dir/\")],\n", + " outputs=Artifact(name=\"json-output\", path=\"/output-dir/output.json\"),\n", + ")\n", + "def do_division(a: int, b: int):\n", + " div = a / b\n", + " intdiv = a // b\n", + " remain = a % b\n", + " dictionary_of_results = {\n", + " \"divide\": div,\n", + " \"quotient\": intdiv,\n", + " \"remainder\": remain,\n", + " }\n", + " with open(\"/output-dir/output.json\", \"w\") as otpt:\n", + " json.dump(dictionary_of_results, otpt)\n", + "\n", + "\n", + "with Workflow(\n", + " generate_name=\"hera-division-\", # when running on graphql this should be name\n", + " entrypoint=\"divide\",\n", + " api_version=\"argoproj.io/v1alpha1\",\n", + " kind=\"Workflow\", # ClusterWorkflowTemplate\", when on graphql\n", + " labels={\"workflows.diamond.ac.uk/science-group-examples\": \"true\"},\n", + " annotations={\n", + " \"workflows.argoproj.io/title\": \"Division via hera test\",\n", + " \"workflows.argoproj.io/description\": \"\"\"Takes a numerical input and returns\n", + " the remainder, output float, and output string to a json file\"\"\",\n", + " \"workflows.diamond.ac.uk/repository\": \"https://github.com/DiamondLightSource/python-interface-to-workflows\",\n", + " },\n", + " volumes=EmptyDirVolume(name=\"output-dir\", mount_path=\"/output-dir\"),\n", + ") as w:\n", + " with Steps(name=\"divide\"):\n", + " do_division(name=\"first\", arguments={\"a\": 2, \"b\": 5})\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "04708f46", + "metadata": {}, + "outputs": [], + "source": [ + "with open(\"../../templates/division_from_jupyter.yaml\", \"w\") as div:\n", + " div.write(w.to_yaml()) # pyright: ignore[reportUnknownMemberType]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7e9f88cb", + "metadata": {}, + "outputs": [], + "source": [ + "from python_interface_to_workflows.submit_to_argo import submit_workflow_to_argo\n", + "\n", + "submit_workflow_to_argo(w)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "python-interface-to-workflows (3.11.x)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.-1" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/src/python_interface_to_workflows/workflow_definitions/notebooks/notebook_example.ipynb b/src/python_interface_to_workflows/workflow_definitions/notebooks/notebook_example.ipynb new file mode 100644 index 0000000..d1592a7 --- /dev/null +++ b/src/python_interface_to_workflows/workflow_definitions/notebooks/notebook_example.ipynb @@ -0,0 +1,251 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "1e3146f1", + "metadata": {}, + "source": [ + "# Running in VSCode:\n", + "\n", + "1. Set kernal to python-interface-to-workflows 3.11.x\n", + "2. Hit F1, run Jupyter: Import Notebook to Script\n", + "3. Click notebook_example.ipynb\n", + "4. Run the cells sequentially" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "494174ef", + "metadata": {}, + "outputs": [], + "source": [ + "from hera.workflows import (\n", + " DAG,\n", + " Artifact,\n", + " Parameter,\n", + " Volume,\n", + " Workflow,\n", + " script, # pyright: ignore[reportUnknownVariableType]\n", + ")\n", + "from hera.workflows import models as m\n", + "from hera.workflows.archive import NoneArchiveStrategy\n", + "\n", + "\n", + "@script(\n", + " command=[\"python\"],\n", + " volume_mounts=[m.VolumeMount(name=\"tmpdir\", mount_path=\"/tmp\")],\n", + ")\n", + "def install_dependencies():\n", + " import subprocess\n", + "\n", + " print(\"creating venv\")\n", + "\n", + " subprocess.check_call([\"python\", \"-m\", \"venv\", \"/tmp/venv\"])\n", + " subprocess.check_call(\n", + " [\"/tmp/venv/bin/pip\", \"install\", \"pillow\", \"h5py\", \"numpy\", \"hera\"]\n", + " )\n", + "\n", + "\n", + "@script(\n", + " command=[\"python\"],\n", + " outputs=Parameter(\n", + " name=\"out-parameters\", value_from=m.ValueFrom(path=\"/tmp/parameters.json\")\n", + " ),\n", + " volume_mounts=[m.VolumeMount(name=\"tmpdir\", mount_path=\"/tmp\")],\n", + ")\n", + "def generate_parameters(\n", + " png: str,\n", + " jpg: str,\n", + " jpeg: str,\n", + " tif: str,\n", + " tiff: str,\n", + "):\n", + " import json\n", + "\n", + " params: list[dict[str, int | list[int] | str] | None] = [\n", + " {\"width\": 500, \"height\": 500, \"weights\": [255, 1, 100], \"extension\": \"png\"}\n", + " if png.lower() == \"true\"\n", + " else None,\n", + " {\"width\": 600, \"height\": 200, \"weights\": [100, 150, 100], \"extension\": \"jpg\"}\n", + " if jpg.lower() == \"true\"\n", + " else None,\n", + " {\"width\": 300, \"height\": 400, \"weights\": [100, 150, 100], \"extension\": \"jpeg\"}\n", + " if jpeg.lower() == \"true\"\n", + " else None,\n", + " {\"width\": 300, \"height\": 200, \"weights\": [230, 100, 1], \"extension\": \"tif\"}\n", + " if tif.lower() == \"true\"\n", + " else None,\n", + " {\"width\": 200, \"height\": 300, \"weights\": [230, 100, 1], \"extension\": \"tiff\"}\n", + " if tiff.lower() == \"true\"\n", + " else None,\n", + " ]\n", + " params_to_write: list[dict[str, int | list[int] | str]] = [\n", + " image_params for image_params in params if image_params is not None\n", + " ]\n", + " with open(\"/tmp/parameters.json\", \"w\") as f:\n", + " json.dump(params_to_write, f)\n", + "\n", + "\n", + "@script(\n", + " command=[\"/tmp/venv/bin/python\"],\n", + " volume_mounts=[m.VolumeMount(name=\"tmpdir\", mount_path=\"/tmp\")],\n", + " outputs=[\n", + " Parameter(\n", + " name=\"out-paths\",\n", + " value_from=m.ValueFrom(\n", + " path=\"/tmp/{{inputs.parameters.extension}}-path.json\"\n", + " ),\n", + " ),\n", + " Artifact(\n", + " name=\"{{inputs.parameters.extension}}-image\",\n", + " path=\"/tmp/{{inputs.parameters.extension}}-image.{{inputs.parameters.extension}}\",\n", + " archive=NoneArchiveStrategy(),\n", + " ),\n", + " ],\n", + ")\n", + "def create_image(\n", + " width: int, height: int, weights: tuple[int, int, int], extension: str\n", + "):\n", + " import json\n", + "\n", + " from PIL import Image\n", + "\n", + " def create_pattern(\n", + " width: int,\n", + " height: int,\n", + " weights: tuple[int, int, int],\n", + " ) -> Image.Image:\n", + " print(f\"width: {width}\")\n", + " print(f\"height: {height}\")\n", + " print(f\"RBG weights: {weights}\")\n", + " image = Image.new(\"RGB\", (width, height))\n", + " pixels = image.load()\n", + " for i in range(width):\n", + " for j in range(height):\n", + " pixels[i, j] = ( # pyright: ignore[reportOptionalSubscript]\n", + " (i + j * 50) % weights[0],\n", + " weights[1],\n", + " (i * 300 + j) % weights[2],\n", + " )\n", + " return image\n", + "\n", + " image = create_pattern(width, height, weights)\n", + " path = f\"/tmp/{extension}-image.{extension}\"\n", + " image.save(path)\n", + " with open(f\"/tmp/{extension}-path.json\", \"w\") as f:\n", + " json.dump(path, f)\n", + "\n", + "\n", + "@script(\n", + " command=[\"/tmp/venv/bin/python\"],\n", + " volume_mounts=[m.VolumeMount(name=\"tmpdir\", mount_path=\"/tmp\")],\n", + " outputs=Artifact(\n", + " name=\"hdf5output\",\n", + " path=\"/tmp/images.hdf5\",\n", + " archive=NoneArchiveStrategy(),\n", + " ),\n", + ")\n", + "def to_hdf5(paths: str):\n", + "\n", + " import h5py # pyright: ignore[reportMissingTypeStubs]\n", + " import numpy as np\n", + " from PIL import Image\n", + "\n", + " print(\"creating hdf5 file\")\n", + " with h5py.File(\"/tmp/images.hdf5\", \"w\") as f:\n", + " for i, path in enumerate(paths):\n", + " path = path.strip('\"')\n", + " print(f\"Got {path}\")\n", + " with Image.open(path) as image:\n", + " arr = np.array(image)\n", + " f.create_dataset( # pyright: ignore[reportUnknownMemberType]\n", + " f\"image_{i}\", data=arr, dtype=arr.dtype\n", + " )\n", + " print(\"done\")\n", + "\n", + "\n", + "with Workflow(\n", + " generate_name=\"hera-example-\", # when running on graphql this should be name\n", + " entrypoint=\"workflowentry\",\n", + " api_version=\"argoproj.io/v1alpha1\",\n", + " kind=\"Workflow\", # ClusterWorkflowTemplate\", when on graphql\n", + " labels={\"workflows.diamond.ac.uk/science-group-examples\": \"true\"},\n", + " annotations={\n", + " \"workflows.argoproj.io/title\": \"example remade via hera\",\n", + " \"workflows.argoproj.io/description\": \"\"\"Replicates the functionality of\n", + "example.yaml\"\"\",\n", + " \"workflows.diamond.ac.uk/repository\": \"https://github.com/DiamondLightSource/python-interface-to-workflows\",\n", + " },\n", + " volumes=Volume(name=\"tmpdir\", mount_path=\"/tmp/\", size=\"1Gi\"),\n", + ") as w:\n", + " with DAG(name=\"workflowentry\"):\n", + " install = install_dependencies(name=\"install\")\n", + " params = generate_parameters(\n", + " name=\"params\",\n", + " arguments={\n", + " \"png\": \"True\",\n", + " \"jpg\": \"True\",\n", + " \"jpeg\": \"True\",\n", + " \"tif\": \"True\",\n", + " \"tiff\": \"True\",\n", + " },\n", + " )\n", + " makeimages = create_image(with_param=params.get_parameter(\"out-parameters\"))\n", + " makehdf5 = to_hdf5(\n", + " arguments={\n", + " \"paths\": makeimages.get_parameter(\"out-paths\"),\n", + " }\n", + " )\n", + " [install, params] >> makeimages >> makehdf5 # pyright: ignore\n", + "\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "04708f46", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "with open(\"../../templates/example_from_jupyter.txt\", \"w\") as div:\n", + " div.write(w.to_yaml()) # pyright: ignore[reportUnknownMemberType]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7e9f88cb", + "metadata": {}, + "outputs": [], + "source": [ + "from python_interface_to_workflows.submit_to_argo import submit_workflow_to_argo\n", + "\n", + "submit_workflow_to_argo(w)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "python-interface-to-workflows (3.11.x)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.15" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/tests/test_keycloak_checker.py b/tests/test_keycloak_checker.py index bb5c776..6f6bc21 100644 --- a/tests/test_keycloak_checker.py +++ b/tests/test_keycloak_checker.py @@ -1,12 +1,22 @@ import os -from unittest.mock import MagicMock, patch +from unittest.mock import MagicMock, call, patch from pytest import mark from python_interface_to_workflows.auth.keycloak_checker import set_token_env_variable -@mark.parametrize("dev,port", [(True, 5173), (False, 8000)]) +@mark.parametrize( + "staging,port,return_present", + [ + (True, 5173, True), + (False, 8000, False), + (True, 5173, False), + (False, 8000, True), + ], +) +@patch("python_interface_to_workflows.auth.keycloak_checker.dotenv.load_dotenv") +@patch("python_interface_to_workflows.auth.keycloak_checker.dotenv.set_key") @patch("python_interface_to_workflows.auth.keycloak_checker.KeycloakOpenID") @patch("python_interface_to_workflows.auth.keycloak_checker.generate_code_verifier") @patch("python_interface_to_workflows.auth.keycloak_checker.generate_code_challenge") @@ -16,25 +26,50 @@ def test_set_token_env_variable( mock_gen_code_challenge: MagicMock, mock_gen_code_verifier: MagicMock, mock_gen_keycloak_id: MagicMock, - dev: bool, + mock_set_key: MagicMock, + mock_load_env: MagicMock, + staging: bool, port: int, + return_present: bool, ): mock_gen_code_verifier.return_value = "verifier" mock_gen_code_challenge.return_value = ("challenge", "S256") os.environ["AUTH"] = "auth_url_code" + os.environ["REFRESHTOKEN"] = "refresh" + keycloak = MagicMock() mock_gen_keycloak_id.return_value = keycloak - + mock_open_auth_url.return_value = return_present keycloak.auth_url.return_value = "https://mock.site" - keycloak.token.return_value = { + token = { "access_token": "fake_token", "refresh_token": "fake_refresh", } - assert set_token_env_variable(dev) == "fake_token" + keycloak.token.return_value = token + keycloak.refresh_token.return_value = token + keycloak.decode_token.return_value = {"exp": 123456789} + assert set_token_env_variable(staging) == "fake_token" + mock_open_auth_url.assert_called_once_with("https://mock.site", port) - keycloak.token.assert_called_once_with( - grant_type="authorization_code", - code="auth_url_code", - redirect_uri=f"http://localhost:{port}/", - code_verifier="verifier", + if return_present: + keycloak.token.assert_called_once_with( + grant_type="authorization_code", + code="auth_url_code", + redirect_uri=f"http://localhost:{port}/", + code_verifier="verifier", + ) + keycloak.refresh_token.assert_not_called() + else: + keycloak.refresh_token.assert_called_once_with("refresh") + keycloak.token.assert_not_called() + mock_set_key.assert_has_calls( + [ + call("src/.env", "EXPIRY", str(123456789 + 1500)), + call("src/.env", "TOKEN", "fake_token"), + call("src/.env", "REFRESHTOKEN", "fake_refresh"), + ] + ) + mock_load_env.assert_called_once_with( + dotenv_path="src/.env", + override=True, ) diff --git a/tests/test_open_auth_url.py b/tests/test_open_auth_url.py index 59fa0d3..e05fb49 100644 --- a/tests/test_open_auth_url.py +++ b/tests/test_open_auth_url.py @@ -7,22 +7,45 @@ ) +@patch("python_interface_to_workflows.auth.open_auth_url.dotenv.set_key") +@patch("python_interface_to_workflows.auth.open_auth_url.dotenv.load_dotenv") +@patch("python_interface_to_workflows.auth.open_auth_url.time.time") @patch("python_interface_to_workflows.auth.open_auth_url.webbrowser.open") @patch("python_interface_to_workflows.auth.open_auth_url._ReusingHTTPServer") def test_open_auth_url_normal_function( mock_http_server: MagicMock, mock_open_browser: MagicMock, + mock_time: MagicMock, + mock_load_env: MagicMock, + mock_set_key: MagicMock, ): + mock_time.return_value = 100 + os.environ["EXPIRY"] = "" + server = mock_http_server.return_value server.auth_code = "this_is_your_code" - open_auth_url("url", 5173) + + assert open_auth_url("url", 5173) is True + + mock_load_env.assert_called_once_with( + dotenv_path="src/.env", + override=True, + ) server.handle_request.assert_called_once() mock_open_browser.assert_called_once_with("url") + mock_set_key.assert_called_once_with( + "src/.env", + "AUTH", + "this_is_your_code", + ) server.socket.shutdown.assert_called_once() server.server_close.assert_called_once() assert os.environ["AUTH"] == "this_is_your_code" +@patch("python_interface_to_workflows.auth.open_auth_url.dotenv.set_key") +@patch("python_interface_to_workflows.auth.open_auth_url.dotenv.load_dotenv") +@patch("python_interface_to_workflows.auth.open_auth_url.time.time") @patch("python_interface_to_workflows.auth.open_auth_url.exit") @patch("python_interface_to_workflows.auth.open_auth_url.webbrowser.open") @patch("python_interface_to_workflows.auth.open_auth_url._ReusingHTTPServer") @@ -30,18 +53,48 @@ def test_open_auth_url_raises_error( mock_http_server: MagicMock, mock_open_browser: MagicMock, mock_exit: MagicMock, + mock_time: MagicMock, + mock_load_env: MagicMock, + mock_set_key: MagicMock, ): + mock_time.return_value = 100 + os.environ["EXPIRY"] = "" + server = mock_http_server.return_value - server.auth_code = "this_is_your_code" server.handle_request.side_effect = OSError - open_auth_url("url", 5173) + + assert open_auth_url("url", 5173) is True mock_open_browser.assert_called_once_with("url") + mock_load_env.assert_called_once() assert os.environ["AUTH"] == "" mock_exit.assert_called_once_with(1) + mock_set_key.assert_not_called() server.socket.shutdown.assert_called_once() server.server_close.assert_called_once() +@patch("python_interface_to_workflows.auth.open_auth_url.webbrowser.open") +@patch("python_interface_to_workflows.auth.open_auth_url.dotenv.load_dotenv") +@patch("python_interface_to_workflows.auth.open_auth_url.time.time") +@patch("python_interface_to_workflows.auth.open_auth_url._ReusingHTTPServer") +def test_open_auth_url_refresh_token( + mock_http_server: MagicMock, + mock_time: MagicMock, + mock_load_env: MagicMock, + mock_open_browser: MagicMock, +): + mock_time.return_value = 100 + os.environ["EXPIRY"] = "200" + assert open_auth_url("url", 5173) is False + + mock_load_env.assert_called_once_with( + dotenv_path="src/.env", + override=True, + ) + mock_http_server.assert_not_called() + mock_open_browser.assert_not_called() + + def test_handler_normal_function(): handler = CallbackHandler.__new__(CallbackHandler) handler.path = "/?code=this_is_your_code"