fractal-task-tools 0.0.3__tar.gz → 0.0.5__tar.gz

{fractal_task_tools-0.0.3/src/fractal_task_tools.egg-info → fractal_task_tools-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: fractal-task-tools
-Version: 0.0.3
+Version: 0.0.5
 Summary: Shared tools for Fractal tasks
 Author-email: Tommaso Comparin <tommaso.comparin@exact-lab.it>
 License: BSD-3-Clause

{fractal_task_tools-0.0.3 → fractal_task_tools-0.0.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-task-tools"
-version = "0.0.3"
+version = "0.0.5"
 description = "Shared tools for Fractal tasks"
 authors = [
     {name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it"},
@@ -34,7 +34,7 @@ build-backend = "setuptools.build_meta"
 fractal-manifest = "fractal_task_tools._cli:main"
 
 [tool.bumpver]
-current_version = "0.0.3"
+current_version = "0.0.5"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

{fractal_task_tools-0.0.3 → fractal_task_tools-0.0.5}/src/fractal_task_tools/__init__.py

@@ -2,4 +2,4 @@ import logging
 
 logging.basicConfig(level=logging.INFO)
 
-__VERSION__ = "0.0.3"
+__VERSION__ = "0.0.5"

{fractal_task_tools-0.0.3 → fractal_task_tools-0.0.5}/src/fractal_task_tools/task_models.py

@@ -2,13 +2,12 @@ from typing import Any
 from typing import Optional
 
 from pydantic import BaseModel
+from pydantic import ConfigDict
 from pydantic import Field
 
 
 class _BaseTask(BaseModel):
-    class Config:
-        arbitrary_types_allowed = True
-        extra = "forbid"
+    model_config = ConfigDict(extra="forbid", arbitrary_types_allowed=True)
 
     name: str
     executable: str

fractal_task_tools-0.0.5/src/fractal_task_tools/task_wrapper.py

@@ -0,0 +1,71 @@
+"""
+Standard input/output interface for tasks.
+"""
+import json
+import logging
+from argparse import ArgumentParser
+from json import JSONEncoder
+from pathlib import Path
+from typing import Optional
+
+
+class TaskParameterEncoder(JSONEncoder):
+    """
+    Custom JSONEncoder that transforms Path objects to strings.
+
+    Ref https://docs.python.org/3/library/json.html
+    """
+
+    def default(self, obj):
+        if isinstance(obj, Path):
+            return obj.as_posix()
+        return super().default(obj)
+
+
+def run_fractal_task(
+    *,
+    task_function: callable,
+    logger_name: Optional[str] = None,
+):
+    """
+    Implement standard task interface and call task_function.
+
+    Args:
+        task_function: the callable function that runs the task.
+        logger_name: TBD
+    """
+
+    # Parse `-j` and `--metadata-out` arguments
+    parser = ArgumentParser()
+    parser.add_argument(
+        "--args-json", help="Read parameters from json file", required=True
+    )
+    parser.add_argument(
+        "--out-json",
+        help="Output file to redirect serialised returned data",
+        required=True,
+    )
+    parsed_args = parser.parse_args()
+
+    # Set logger
+    logger = logging.getLogger(logger_name)
+
+    # Preliminary check
+    if Path(parsed_args.out_json).exists():
+        logger.error(
+            f"Output file {parsed_args.out_json} already exists. Terminating"
+        )
+        exit(1)
+
+    # Read parameters dictionary
+    with open(parsed_args.args_json, "r") as f:
+        pars = json.load(f)
+
+    # Run task
+    logger.info(f"START {task_function.__name__} task")
+    metadata_update = task_function(**pars)
+    logger.info(f"END {task_function.__name__} task")
+
+    # Write output metadata to file, with custom JSON encoder
+    with open(parsed_args.out_json, "w") as fout:
+        json.dump(metadata_update, fout, cls=TaskParameterEncoder, indent=2)

{fractal_task_tools-0.0.3 → fractal_task_tools-0.0.5/src/fractal_task_tools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: fractal-task-tools
-Version: 0.0.3
+Version: 0.0.5
 Summary: Shared tools for Fractal tasks
 Author-email: Tommaso Comparin <tommaso.comparin@exact-lab.it>
 License: BSD-3-Clause

{fractal_task_tools-0.0.3 → fractal_task_tools-0.0.5}/src/fractal_task_tools.egg-info/SOURCES.txt

@@ -12,6 +12,7 @@ src/fractal_task_tools/_signature_constraints.py
 src/fractal_task_tools/_task_docs.py
 src/fractal_task_tools/_titles.py
 src/fractal_task_tools/task_models.py
+src/fractal_task_tools/task_wrapper.py
 src/fractal_task_tools.egg-info/PKG-INFO
 src/fractal_task_tools.egg-info/SOURCES.txt
 src/fractal_task_tools.egg-info/dependency_links.txt
@@ -20,4 +21,7 @@ src/fractal_task_tools.egg-info/requires.txt
 src/fractal_task_tools.egg-info/top_level.txt
 tests/test_create_schema_for_single_task.py
 tests/test_extract_function.py
+tests/test_normalize_package_name.py
+tests/test_task_models.py
+tests/test_task_wrapper.py
 tests/test_unit_lib_descriptions.py

fractal_task_tools-0.0.5/tests/test_normalize_package_name.py

@@ -0,0 +1,7 @@
+from fractal_task_tools._package_name_tools import normalize_package_name
+
+
+def test_normalize_package_name():
+    raw_name = "Aa-_.Aa"
+    normalized_name = "aa_aa"
+    assert normalize_package_name(raw_name) == normalized_name

fractal_task_tools-0.0.5/tests/test_task_models.py

@@ -0,0 +1,47 @@
+from fractal_task_tools.task_models import CompoundTask
+from fractal_task_tools.task_models import NonParallelTask
+from fractal_task_tools.task_models import ParallelTask
+
+NAME = "name"
+EXECUTABLE = "executable"
+EXECUTABLE_INIT = "executable_init"
+META = {"some": "thing"}
+META_INIT = {"some": "thing-init"}
+
+
+def test_compound_task_model():
+    t = CompoundTask(
+        name=NAME,
+        executable_init=EXECUTABLE_INIT,
+        meta_init=META_INIT,
+        executable=EXECUTABLE,
+        meta=META,
+    )
+    assert t.executable_non_parallel == EXECUTABLE_INIT
+    assert t.meta_non_parallel == META_INIT
+    assert t.executable_parallel == EXECUTABLE
+    assert t.meta_parallel == META
+
+
+def test_non_parallel_task_model():
+    t = NonParallelTask(
+        name=NAME,
+        executable=EXECUTABLE_INIT,
+        meta=META_INIT,
+    )
+    assert t.executable_non_parallel == EXECUTABLE_INIT
+    assert t.meta_non_parallel == META_INIT
+    assert t.executable_parallel is None
+    assert t.meta_parallel is None
+
+
+def test_parallel_task_model():
+    t = ParallelTask(
+        name=NAME,
+        executable=EXECUTABLE,
+        meta=META,
+    )
+    assert t.executable_non_parallel is None
+    assert t.meta_non_parallel is None
+    assert t.executable_parallel == EXECUTABLE
+    assert t.meta_parallel == META

fractal_task_tools-0.0.5/tests/test_task_wrapper.py

@@ -0,0 +1,88 @@
+import json
+from datetime import datetime
+from pathlib import Path
+
+import pytest
+from fractal_task_tools.task_wrapper import run_fractal_task
+from pydantic import ValidationError
+from pydantic.validate_call_decorator import validate_call
+
+TASK_OUTPUT = {
+    "some": "thing",
+    "path": Path("/something"),
+}
+
+SERIALIZED_TASK_OUTPUT = {
+    "some": "thing",
+    "path": "/something",
+}
+
+
+@validate_call
+def fake_task(zarr_url: str, parameter: float):
+    return TASK_OUTPUT
+
+
+@validate_call
+def fake_task_invalid_output(zarr_url: str, parameter: float):
+    return dict(non_json_serializable=datetime.now())
+
+
+def test_run_fractal_task(tmp_path, monkeypatch, caplog):
+
+    ARGS_PATH = tmp_path / "args.json"
+    METADIFF_PATH = tmp_path / "metadiff.json"
+
+    # Mock argparse.ArgumentParser
+    class MockArgumentParser:
+        def add_argument(self, *args, **kwargs):
+            pass
+
+        def parse_args(self, *args, **kwargs):
+            class Args(object):
+                def __init__(self):
+                    self.args_json = str(ARGS_PATH)
+                    self.out_json = str(METADIFF_PATH)
+
+            return Args()
+
+    import fractal_task_tools.task_wrapper  # noqa: F401
+
+    monkeypatch.setattr(
+        "fractal_task_tools.task_wrapper.ArgumentParser",
+        MockArgumentParser,
+    )
+
+    # Success
+    args = dict(zarr_url="/somewhere", parameter=1.0)
+    with ARGS_PATH.open("w") as f:
+        json.dump(args, f, indent=2)
+    function_output = run_fractal_task(task_function=fake_task)
+    assert function_output is None
+    with METADIFF_PATH.open("r") as f:
+        task_output = json.load(f)
+    assert task_output == SERIALIZED_TASK_OUTPUT
+
+    # Failure (metadiff file already exists)
+    caplog.clear()
+    with pytest.raises(SystemExit):
+        run_fractal_task(task_function=fake_task)
+    assert "already exists" in caplog.text
+
+    # Failure (invalid output)
+    METADIFF_PATH.unlink()
+    with pytest.raises(
+        TypeError,
+        match="datetime is not JSON serializable",
+    ):
+        run_fractal_task(task_function=fake_task_invalid_output)
+
+    # Failure (invalid input)
+    METADIFF_PATH.unlink()
+    args = dict(zarr_url="/somewhere", parameter=None)
+    with ARGS_PATH.open("w") as f:
+        json.dump(args, f, indent=2)
+    with pytest.raises(
+        ValidationError, match="validation error for fake_task"
+    ):
+        run_fractal_task(task_function=fake_task)