fractal-task-tools 0.0.3__py3-none-any.whl → 0.0.5__py3-none-any.whl

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/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/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.dist-info → fractal_task_tools-0.0.5.dist-info}/METADATA

@@ -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.dist-info → fractal_task_tools-0.0.5.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_task_tools/__init__.py,sha256=1YpKCxwIh1hw8i8urrjbhHmN7-4tKR_58qdmgN3lhU8,79
+fractal_task_tools/__init__.py,sha256=MnFTaW45JfhnCV-zkWHY7mQ_mXPAF8ISIYUTznGWs2M,79
 fractal_task_tools/_args_schemas.py,sha256=Ka5IAAEdC7xg03ZHMl5jFbv4Sk8JR1QKbxFl7soevlQ,7829
 fractal_task_tools/_cli.py,sha256=6x2wWG6cFTw0m8HsxLmeboT3AMNf7ofhAI2kWEZMkx8,1849
 fractal_task_tools/_create_manifest.py,sha256=DTl1gV4XvQy_ArOAOSUzKLcTHYuE_un94dBvpfdkeeI,6922
@@ -8,10 +8,11 @@ fractal_task_tools/_pydantic_generatejsonschema.py,sha256=qZuID7YUXOdAcL8OqsWjNF
 fractal_task_tools/_signature_constraints.py,sha256=RzJwoL-NMD0HXEACR4_4aD8OOc59lxqEreT7oTc6xJo,3188
 fractal_task_tools/_task_docs.py,sha256=aEXozSKf3a7weOwJMHyTVJTvHlCKgDr1qoU-AAO3bZI,3401
 fractal_task_tools/_titles.py,sha256=GLWn-06fgQD6qzOM75H59EV0MMCXc8jVpHqGanYzNbw,3000
-fractal_task_tools/task_models.py,sha256=xTbdk3lf6T70o8idEWw-bdjA2dDz0KDIrBjdoh_A9Lc,2243
-fractal_task_tools-0.0.3.dist-info/LICENSE,sha256=1SGAsQ3Jm_nIU7c2TgtTZe_IOKjm9BDsrcf2r98xrdk,1584
-fractal_task_tools-0.0.3.dist-info/METADATA,sha256=cIlag9pQq6VO-VPwAhKd5Og7R6qg5LwqrcYn5y5Wygc,4212
-fractal_task_tools-0.0.3.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
-fractal_task_tools-0.0.3.dist-info/entry_points.txt,sha256=zE4qv7QhuiqN6DaPkmJV18X1xyYoUi0HIJ-uAg2M6TU,66
-fractal_task_tools-0.0.3.dist-info/top_level.txt,sha256=2VBpiMDIBMJGOEPiHHX3njYEZGLhr4L0nu8vfkcNVzw,19
-fractal_task_tools-0.0.3.dist-info/RECORD,,
+fractal_task_tools/task_models.py,sha256=kgvEv5NQD8e8I9tyaFrnvxUxbKm6vH63r-cnID1jHE8,2269
+fractal_task_tools/task_wrapper.py,sha256=dhphKgxDm4EUxZnsrAy20hJPD6bGdqx7tNg9N_QzlCo,1878
+fractal_task_tools-0.0.5.dist-info/LICENSE,sha256=1SGAsQ3Jm_nIU7c2TgtTZe_IOKjm9BDsrcf2r98xrdk,1584
+fractal_task_tools-0.0.5.dist-info/METADATA,sha256=rlEyaK2tRYJxgoVaFyCdAbs0TNhk3t2s6c75z9Utj0o,4212
+fractal_task_tools-0.0.5.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+fractal_task_tools-0.0.5.dist-info/entry_points.txt,sha256=zE4qv7QhuiqN6DaPkmJV18X1xyYoUi0HIJ-uAg2M6TU,66
+fractal_task_tools-0.0.5.dist-info/top_level.txt,sha256=2VBpiMDIBMJGOEPiHHX3njYEZGLhr4L0nu8vfkcNVzw,19
+fractal_task_tools-0.0.5.dist-info/RECORD,,