Merge pull request #18 from wtsi-npg/devel

Release 0.2.0

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Referenced from:
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

CHANGELOG.md

@@ -1,12 +1,20 @@
-# Change Log for npg_porch Project
+<!-- markdownlint-disable MD024 -->
+# Change Log for npg_porch_cli Project
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/).
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## [Unreleased]
+## [0.2.0] - 2024-12-18
+
+### Added
+
+* Added .github/dependabot.yml file to auto-update GitHub actions
+* Implemented the `create_token` action. Provided the caller has an admin token,
+  this action generates and returns a new pipeline-specific token.
+* Used npg-python-lib to read Porch config
 
 ## [0.1.0] - 2024-07-23
 
 ### Added
 
-# Initial project scaffold, code and tests
+* Initial project scaffold, code and tests

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "npg_porch_cli"
-version = "0.1.0"
+version = "0.2.0"
 authors = [
     "Marina Gourtovaia",
     "Kieron Taylor",
@@ -11,11 +11,12 @@ readme = "README.md"
 license = "GPL-3.0-or-later"
 
 [tool.poetry.scripts]
-npg_porch_client = "npg_porch_cli.api_cli_user:run" 
+npg_porch_client = "npg_porch_cli.api_cli_user:run"
 
 [tool.poetry.dependencies]
 python = "^3.10"
 requests = "^2.31.0"
+npg-python-lib = { git="https://github.com/wtsi-npg/npg-python-lib", tag="0.3.4"}
 
 [tool.poetry.dev-dependencies]
 black = "^22.3.0"

src/npg_porch_cli/api.py

@@ -162,18 +162,24 @@ def list_client_actions() -> list[str]:
     return sorted(_PORCH_CLIENT_ACTIONS.keys())
 
 
-def send(action: PorchAction, pipeline: Pipeline = None) -> dict | list:
+def send(
+    action: PorchAction, pipeline: Pipeline = None, description: str | None = None
+) -> dict | list:
     """Sends a request to the porch API server.
 
     Sends a request to the porch API server to perform an action defined
     by the `action` attribute of the `action` argument. The context of the
     query is defined by the pipeline argument.
 
+    See also send_request for SSL validation guidance
+
     Args:
       action:
         npg_porch_cli.api.PorchAction object
       pipeline:
         npg_porch_cli.api.Pipeline object
+      description:
+        A description for the new token, optional
 
     Returns:
       The server's response is returned as a Python data structure.
@@ -183,6 +189,8 @@ def send(action: PorchAction, pipeline: Pipeline = None) -> dict | list:
     function = _PORCH_CLIENT_ACTIONS[action.action]
     if action.action == "list_pipelines":
         return function(action=action)
+    elif action.action == "create_token":
+        return function(action=action, pipeline=pipeline, description=description)
     return function(action=action, pipeline=pipeline)
 
 
@@ -333,13 +341,39 @@ def update_task(action: PorchAction, pipeline: Pipeline):
     )
 
 
+def create_token(action: PorchAction, pipeline: Pipeline, description: str):
+    """Creates a new token for the pipeline.
+
+    Args:
+      action:
+        npg_porch_cli.api.PorchAction object
+      pipeline:
+        npg_porch_cli.api.Pipeline object
+      description:
+        A short token description
+
+    Returns:
+      A dictionary containing a new token.
+    """
+
+    if not description:
+        raise TypeError("Token description should be given")
+
+    return send_request(
+        validate_ca_cert=action.validate_ca_cert,
+        url=urljoin(action.porch_url, f"pipelines/{pipeline.name}/token/{description}"),
+        method="POST",
+    )
+
+
 _PORCH_CLIENT_ACTIONS = {
     "list_tasks": list_tasks,
     "list_pipelines": list_pipelines,
     "add_pipeline": add_pipeline,
     "add_task": add_task,
     "claim_task": claim_task,
     "update_task": update_task,
+    "create_token": create_token,
 }
 
 
@@ -358,8 +392,8 @@ def send_request(
     Args:
       validate_ca_cert:
         A boolean flag defining whether the server CA certificate
-        will be validated. If set to True, SSL_CERT_FILE environment
-        variable should be set.
+        will be validated. If set to True, REQUESTS_CA_BUNDLE environment
+        variable should be set, for example to /etc/ssl/certs/ca-certificates.crt
       url:
         A URL to send the request to.
       method:

src/npg_porch_cli/api_cli_user.py

@@ -43,6 +43,7 @@ def run():
         list_tasks
         list_pipelines
         add_pipeline
+        create_token
         add_task
         claim_task
         update_task
@@ -54,13 +55,15 @@ def run():
     `--pipeline_name` is defined, `list_tasks` returns a list of tasks for
     this pipeline, otherwise all registered tasks are returned.
 
-    All non-list actions require all `--pipeline`, `pipeline_url` and
+    All non-list actions require `--pipeline`, `pipeline_url` and
     `--pipeline_version` defined.
 
     The `add_task` and `update_task` actions require the `--task_json` to
     be defined. In addition to this, for the `update_task` action `--status`
     should be defined.
 
+    The `create_token` action requires that the `--description` is defined.
+
     NPG_PORCH_TOKEN environment variable should be set to the value of
     either an admin or project-specific token.
 
@@ -94,6 +97,7 @@ def run():
     parser.add_argument("--pipeline", type=str, help="Pipeline name, optional")
     parser.add_argument("--task_json", type=str, help="Task as JSON, optional")
     parser.add_argument("--status", type=str, help="New status to set, optional")
+    parser.add_argument("--description", type=str, help="Token description, optional")
 
     args = parser.parse_args()
 
@@ -110,4 +114,9 @@ def run():
             name=args.pipeline, uri=args.pipeline_url, version=args.pipeline_version
         )
 
-    print(json.dumps(send(action=action, pipeline=pipeline), indent=2))
+    print(
+        json.dumps(
+            send(action=action, pipeline=pipeline, description=args.description),
+            indent=2,
+        )
+    )

src/npg_porch_cli/config.py

@@ -0,0 +1,52 @@
+from dataclasses import dataclass
+from os import R_OK, access
+from os.path import isfile
+
+from npg.conf import IniData
+
+
+@dataclass(frozen=True, kw_only=True)
+class PorchClientConfig:
+    """
+    Suggested config file content for interacting with a Porch server instance
+    """
+
+    api_url: str
+    pipeline_name: str
+    pipeline_uri: str
+    pipeline_version: str
+    npg_porch_token: str
+
+
+def get_config_data(
+    conf_file_path: str, conf_file_section: str = "PORCH"
+) -> PorchClientConfig:
+    """
+    Parses a configuration file and returns its content.
+
+    Args:
+
+      conf_file_path:
+        A configuration file with database connection details.
+      conf_file_section:
+        The section of the configuration file. Optional. Should be defined
+        for 'ini' files.
+
+    Returns:
+      For an 'ini' file returns the content of the given section of the file as
+      a dictionary.
+      For a 'json' file, if the conf_file_section argument is not defined, the
+      content of a file as a Python object is returned. If the conf_file_section
+      argument is defined, the object returned by the parser is assumed to be
+      a dictionary that has the value of the 'conf_file_section' argument as a key.
+      The value corresponding to this key is returned.
+    """
+
+    if isfile(conf_file_path) and access(conf_file_path, R_OK):
+        porch_conf = IniData(PorchClientConfig).from_file(
+            conf_file_path, conf_file_section
+        )
+    else:
+        raise FileNotFoundError(f"{conf_file_path} is not present or cannot be read")
+
+    return porch_conf

tests/data/conf.ini

@@ -0,0 +1,17 @@
+[STUFF]
+
+logging = INFO
+
+[PORCH]
+
+api_url = https://porch.dnapipelines.sanger.ac.uk
+pipeline_name = test_pipeline
+pipeline_uri = https://test.pipeline.com
+pipeline_version = 9.9.9
+npg_porch_token = 0123456789abcdef0123456789abcdef
+
+[PARTIALPORCH]
+
+api_url = https://porch.dnapipelines.sanger.ac.uk
+pipeline_name = test_pipeline
+pipeline_uri = https://test.pipeline.com

tests/test_api.py

@@ -51,6 +51,7 @@ def test_listing_actions():
         "add_pipeline",
         "add_task",
         "claim_task",
+        "create_token",
         "list_pipelines",
         "list_tasks",
         "update_task",
@@ -76,8 +77,8 @@ def test_porch_action_class(monkeypatch):
         PorchAction(porch_url=url, action="list_tools")
     assert (
         e.value.args[0] == "Action 'list_tools' is not valid. "
-        "Valid actions: add_pipeline, add_task, claim_task, list_pipelines, "
-        "list_tasks, update_task"
+        "Valid actions: add_pipeline, add_task, claim_task, create_token, "
+        "list_pipelines, list_tasks, update_task"
     )
 
     pa = PorchAction(porch_url=url, action="list_tasks")
@@ -247,3 +248,29 @@ def mock_get_200(*args, **kwargs):
             porch_url=url, action="update_task", task_input=task, task_status="DONE"
         )
         assert send(action=pa, pipeline=p) == response_data
+
+    with monkeypatch.context() as mkp:
+        response_data = {
+            "name": "p1",
+            "description": "for my pipeline",
+            "token": "ccceddd450aaa",
+        }
+
+        def mock_get_200(*args, **kwargs):
+            return MockPorchResponse(response_data, 200)
+
+        mkp.setattr(requests, "request", mock_get_200)
+
+        pa = PorchAction(porch_url=url, action="create_token")
+
+        error_message = "Token description should be given"
+        with pytest.raises(TypeError) as e:
+            send(action=pa, pipeline=p)
+            assert e.value.args[0] == error_message
+        with pytest.raises(TypeError) as e:
+            send(action=pa, pipeline=p, description="")
+            assert e.value.args[0] == error_message
+
+        assert (
+            send(action=pa, pipeline=p, description="for my pipeline") == response_data
+        )

tests/test_porch_client_config.py

@@ -0,0 +1,17 @@
+from pytest import raises
+
+from npg_porch_cli.config import PorchClientConfig, get_config_data
+
+
+def test_conf_obj():
+    config_obj = get_config_data("tests/data/conf.ini")
+    assert config_obj.pipeline_name == "test_pipeline"
+    assert config_obj.pipeline_version == "9.9.9"
+
+    assert type(config_obj) is PorchClientConfig
+
+    with raises(FileNotFoundError, match="notafile is not present or cannot be read"):
+        get_config_data("notafile", conf_file_section="ABSENT")
+
+    with raises(TypeError, match="missing 2 required keyword-only arguments"):
+        get_config_data("tests/data/conf.ini", conf_file_section="PARTIALPORCH")