fractal-task-tools 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl

fractal_task_tools/__init__.py

@@ -2,4 +2,4 @@ import logging
 
 logging.basicConfig(level=logging.INFO)
 
-__VERSION__ = "0.0.2"
+__VERSION__ = "0.0.4"

fractal_task_tools/_cli.py

@@ -1,7 +1,7 @@
 import argparse as ap
 import sys
 
-from fractal_task_tools._create_manifest import check_manifest_unchanged
+from fractal_task_tools._create_manifest import check_manifest
 from fractal_task_tools._create_manifest import create_manifest
 from fractal_task_tools._create_manifest import write_manifest_to_file
 
@@ -66,7 +66,7 @@ def main():
             raw_package_name=args.package,
             task_list_path=args.task_list_path,
         )
-        check_manifest_unchanged(
+        check_manifest(
             raw_package_name=args.package,
             manifest=manifest,
         )

fractal_task_tools/_create_manifest.py

@@ -3,6 +3,8 @@ Generate JSON schemas for task arguments and combine them into a manifest.
 """
 import json
 import logging
+import os
+import sys
 from importlib import import_module
 from pathlib import Path
 from typing import Any
@@ -157,17 +159,26 @@ def write_manifest_to_file(
         raw_package_name:
         manifest: The manifest object
     """
+    logging.info("[write_manifest_to_file] START")
+
     package_name = normalize_package_name(raw_package_name)
+    logging.info(f"[write_manifest_to_file] {package_name=}")
+
     imported_package = import_module(package_name)
     package_root_dir = Path(imported_package.__file__).parent
-    manifest_path = package_root_dir / MANIFEST_FILENAME
-    with manifest_path.open("w") as f:
+    manifest_path = (package_root_dir / MANIFEST_FILENAME).as_posix()
+    logging.info(f"[write_manifest_to_file] {os.getcwd()=}")
+    logging.info(f"[write_manifest_to_file] {package_root_dir=}")
+    logging.info(f"[write_manifest_to_file] {manifest_path=}")
+
+    with open(manifest_path, "w") as f:
         json.dump(manifest, f, indent=2)
         f.write("\n")
-    logging.info(f"Manifest stored in {manifest_path.as_posix()}")
+
+    logging.info("[write_manifest_to_file] END")
 
 
-def check_manifest_unchanged(
+def check_manifest(
     *,
     raw_package_name: str,
     manifest: str,
@@ -179,12 +190,25 @@ def check_manifest_unchanged(
         raw_package_name:
         manifest: The manifest object
     """
+
     package_name = normalize_package_name(raw_package_name)
+    logging.info(f"[check_manifest] {package_name=}")
+
     imported_package = import_module(package_name)
     package_root_dir = Path(imported_package.__file__).parent
-    manifest_path = package_root_dir / MANIFEST_FILENAME
-    with manifest_path.open("f") as f:
+    manifest_path = (package_root_dir / MANIFEST_FILENAME).as_posix()
+    logging.info(f"[check_manifest] {os.getcwd()=}")
+    logging.info(f"[check_manifest] {package_root_dir=}")
+    logging.info(f"[check_manifest] {manifest_path=}")
+
+    with open(manifest_path, "r") as f:
         old_manifest = json.load(f)
-    logging.info(f"Manifest read from {manifest_path.as_posix()}")
-    if manifest != old_manifest:
-        raise ValueError("New/old manifests differ")
+    if manifest == old_manifest:
+        logging.info("[check_manifest] On-disk manifest is up to date.")
+    else:
+        logging.error("[check_manifest] On-disk manifest is not up to date.")
+        print(json.dumps(old_manifest, indent=2))
+        print(json.dumps(manifest, indent=2))
+        sys.exit("New/old manifests differ")
+
+    logging.info("[check_manifest] END")

fractal_task_tools/_signature_constraints.py

@@ -3,7 +3,6 @@ import logging
 from importlib import import_module
 from inspect import signature
 from pathlib import Path
-from typing import Callable
 
 from pydantic.v1.decorator import ALT_V_ARGS
 from pydantic.v1.decorator import ALT_V_KWARGS
@@ -25,7 +24,7 @@ def _extract_function(
     function_name: str,
     package_name: str,
     verbose: bool = False,
-) -> Callable:
+) -> callable:
     """
     Extract function from a module with the same name.
 
@@ -58,7 +57,7 @@ def _extract_function(
     return task_function
 
 
-def _validate_function_signature(function: Callable):
+def _validate_function_signature(function: callable):
     """
     Validate the function signature.
 

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-0.0.2.dist-info → fractal_task_tools-0.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: fractal-task-tools
-Version: 0.0.2
+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-0.0.4.dist-info/RECORD

@@ -0,0 +1,18 @@
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+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
+fractal_task_tools/_descriptions.py,sha256=n7WcoIBQ4FEd16BI26iL-Sh6bEQ76jlU32JfJBF4U0A,7566
+fractal_task_tools/_package_name_tools.py,sha256=_UT2cThh742V6M0XT9m0_aByhj5fXRSjATKt_MIXFVg,819
+fractal_task_tools/_pydantic_generatejsonschema.py,sha256=qZuID7YUXOdAcL8OqsWjNFNumOIAgdJillc1lA2cHIY,3136
+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/task_wrapper.py,sha256=IO2wyD1ph23V_xPNGnjtXewuJ4TOGzq3U4KBlEzB4to,1959
+fractal_task_tools-0.0.4.dist-info/LICENSE,sha256=1SGAsQ3Jm_nIU7c2TgtTZe_IOKjm9BDsrcf2r98xrdk,1584
+fractal_task_tools-0.0.4.dist-info/METADATA,sha256=6jYc6G00qJU60AFxYD9kxkBLWpCsDWB03JNvcFeVJGE,4212
+fractal_task_tools-0.0.4.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+fractal_task_tools-0.0.4.dist-info/entry_points.txt,sha256=zE4qv7QhuiqN6DaPkmJV18X1xyYoUi0HIJ-uAg2M6TU,66
+fractal_task_tools-0.0.4.dist-info/top_level.txt,sha256=2VBpiMDIBMJGOEPiHHX3njYEZGLhr4L0nu8vfkcNVzw,19
+fractal_task_tools-0.0.4.dist-info/RECORD,,

fractal_task_tools-0.0.2.dist-info/RECORD

@@ -1,17 +0,0 @@
-fractal_task_tools/__init__.py,sha256=MRGHqa12kl23-BtFENLSAtLR5nzimughL2HEce80xc0,79
-fractal_task_tools/_args_schemas.py,sha256=Ka5IAAEdC7xg03ZHMl5jFbv4Sk8JR1QKbxFl7soevlQ,7829
-fractal_task_tools/_cli.py,sha256=ikEwNVhzvr_X5PY5_s02lH7JvRcuHgjFs-hoIFQjXYo,1869
-fractal_task_tools/_create_manifest.py,sha256=Ses8N5RliTtbvaHGJwTjuE2sGyBCoJUJtcyO7JPX23w,6147
-fractal_task_tools/_descriptions.py,sha256=n7WcoIBQ4FEd16BI26iL-Sh6bEQ76jlU32JfJBF4U0A,7566
-fractal_task_tools/_package_name_tools.py,sha256=_UT2cThh742V6M0XT9m0_aByhj5fXRSjATKt_MIXFVg,819
-fractal_task_tools/_pydantic_generatejsonschema.py,sha256=qZuID7YUXOdAcL8OqsWjNFNumOIAgdJillc1lA2cHIY,3136
-fractal_task_tools/_signature_constraints.py,sha256=1ixh8acxwY5_jRdyn7KfyRDDuwqQQ2R6Zf1xlElheWY,3216
-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-0.0.2.dist-info/LICENSE,sha256=1SGAsQ3Jm_nIU7c2TgtTZe_IOKjm9BDsrcf2r98xrdk,1584
-fractal_task_tools-0.0.2.dist-info/METADATA,sha256=07uk2zPoBCvv5Nv9Sb_k2jNsBw_2xYb-09XUwouo8Ps,4212
-fractal_task_tools-0.0.2.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
-fractal_task_tools-0.0.2.dist-info/entry_points.txt,sha256=zE4qv7QhuiqN6DaPkmJV18X1xyYoUi0HIJ-uAg2M6TU,66
-fractal_task_tools-0.0.2.dist-info/top_level.txt,sha256=2VBpiMDIBMJGOEPiHHX3njYEZGLhr4L0nu8vfkcNVzw,19
-fractal_task_tools-0.0.2.dist-info/RECORD,,