fractal-task-tools 0.0.3__tar.gz → 0.0.4__tar.gz

{fractal_task_tools-0.0.3/src/fractal_task_tools.egg-info → fractal_task_tools-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: fractal-task-tools
-Version: 0.0.3
+Version: 0.0.4
 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-0.0.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-task-tools"
-version = "0.0.3"
+version = "0.0.4"
 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 = "0.0.4"
 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-0.0.4}/src/fractal_task_tools/__init__.py

@@ -2,4 +2,4 @@ import logging
 
 logging.basicConfig(level=logging.INFO)
 
-__VERSION__ = "0.0.3"
+__VERSION__ = "0.0.4"

fractal_task_tools-0.0.4/src/fractal_task_tools/task_wrapper.py

@@ -0,0 +1,73 @@
+"""
+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.
+    """
+
+    def default(self, value):
+        """
+        Subclass implementation of `default`, to serialize Path objects as
+        strings.
+        """
+        if isinstance(value, Path):
+            return value.as_posix()
+        return JSONEncoder.default(self, value)
+
+
+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-0.0.4/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: 0.0.4
 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-0.0.4}/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