wrote cmd_out arg and unittest based on "ls" for shell_cmd

nipype · tclose · May 11, 2023 · May 11, 2023 · May 15, 2023 · May 15, 2023
commit d22d7a1b75d0262d6b0d63a30c0379637aac3046
diff --git a/pydra/mark/__init__.py b/pydra/mark/__init__.py
@@ -1,3 +1,4 @@
 from .functions import annotate, task
+from .shell_commands import cmd_arg, cmd_out
 
-__all__ = ("annotate", "task")
+__all__ = ("annotate", "task", "cmd_arg", "cmd_out")
diff --git a/pydra/mark/shell_commands.py b/pydra/mark/shell_commands.py
@@ -0,0 +1,156 @@
+"""Decorators and helper functions to create ShellCommandTasks used in Pydra workflows"""
+from __future__ import annotations
+import typing as ty
+import attrs
+
+
+def cmd_arg(
+    help_string: str,
+    default: ty.Any = attrs.NOTHING,
+    argstr: str = None,
+    position: int = None,
+    mandatory: bool = False,
+    sep: str = None,
+    allowed_values: list = None,
+    requires: list = None,
+    xor: list = None,
+    copyfile: bool = None,
+    container_path: bool = False,
+    output_file_template: str = None,
+    output_field_name: str = None,
+    keep_extension: bool = True,
+    readonly: bool = False,
+    formatter: ty.Callable = None,
+):
+    """
+    Returns an attrs field with appropriate metadata for it to be added as an argument in
+    a Pydra shell command task definition
+
+    Parameters
+    ------------
+    help_string: str
+        A short description of the input field.
+    default : Any, optional
+        the default value for the argument
+    argstr: str, optional
+        A flag or string that is used in the command before the value, e.g. -v or
+        -v {inp_field}, but it could be and empty string, “”. If … are used, e.g. -v…,
+        the flag is used before every element if a list is provided as a value. If no
+        argstr is used the field is not part of the command.
+    position: int, optional
+        Position of the field in the command, could be nonnegative or negative integer.
+        If nothing is provided the field will be inserted between all fields with
+        nonnegative positions and fields with negative positions.
+    mandatory: bool, optional
+        If True user has to provide a value for the field
10000
, by default it is False
+    sep: str, optional
+        A separator if a list is provided as a value.
+    allowed_values: list, optional
+        List of allowed values for the field.
+    requires: list, optional
+        List of field names that are required together with the field.
+    xor: list, optional
+        List of field names that are mutually exclusive with the field.
+    copyfile: bool, optional
+        If True, a hard link is created for the input file in the output directory. If
+        hard link not possible, the file is copied to the output directory, by default
+        it is False
+    container_path: bool, optional
+        If True a path will be consider as a path inside the container (and not as a
+        local path, by default it is False
+    output_file_template: str, optional
+        If provided, the field is treated also as an output field and it is added to
+        the output spec. The template can use other fields, e.g. {file1}. Used in order
+        to create an output specification.
+    output_field_name: str, optional
+        If provided the field is added to the output spec with changed name. Used in
+        order to create an output specification. Used together with output_file_template
+    keep_extension: bool, optional
+        A flag that specifies if the file extension should be removed from the field value.
+        Used in order to create an output specification, by default it is True
+    readonly: bool, optional
+        If True the input field can’t be provided by the user but it aggregates other
+        input fields (for example the fields with argstr: -o {fldA} {fldB}), by default
+        it is False
+    formatter: function, optional
+        If provided the argstr of the field is created using the function. This function
+        can for example be used to combine several inputs into one command argument. The
+        function can take field (this input field will be passed to the function),
+        inputs (entire inputs will be passed) or any input field name (a specific input
+        field will be sent).
+    """
+
+    metadata = {
+        "help_string": help_string,
+        "argstr": argstr,
+        "position": position,
+        "mandatory": mandatory,
+        "sep": sep,
+        "allowed_values": allowed_values,
+        "requires": requires,
+        "xor": xor,
+        "copyfile": copyfile,
+        "container_path": container_path,
+        "output_file_template": output_file_template,
+        "output_field_name": output_field_name,
+        "keep_extension": keep_extension,
+        "readonly": readonly,
+        "formatter": formatter,
+    }
+
+    return attrs.field(
+        default=default, metadata={k: v for k, v in metadata.items() if v is not None}
+    )
+
+
+def cmd_out(
+    help_string: str,
+    mandatory: bool = False,
+    output_file_template: str = None,
+    output_field_name: str = None,
+    keep_extension: bool = True,
+    requires: list = None,
+    callable: ty.Callable = None,
+):
+    """Returns an attrs field with appropriate metadata for it to be added as an output of
+    a Pydra shell command task definition
+
+    Parameters
+    ----------
+    help_string: str
+        A short description of the input field. The same as in input_spec.
+    mandatory: bool, default: False
+        If True the output file has to exist, otherwise an error will be raised.
+    output_file_template: str, optional
+        If provided the output file name (or list of file names) is created using the
+        template. The template can use other fields, e.g. {file1}. The same as in
+        input_spec.
+    output_field_name: str, optional
+        If provided the field is added to the output spec with changed name. The same as
+        in input_spec. Used together with output_file_template
+    keep_extension: bool, default: True
+        A flag that specifies if the file extension should be removed from the field
+        value. The same as in input_spec.
+    requires: list
+        List of field names that are required to create a specific output. The fields
+        do not have to be a part of the output_file_template and if any field from the
+        list is not provided in the input, a NOTHING is returned for the specific output.
+        This has a different meaning than the requires form the input_spec.
+    callable: Callable
+        If provided the output file name (or list of file names) is created using the
+        function. The function can take field (the specific output field will be passed
+        to the function), output_dir (task output_dir will be used), stdout, stderr
+        (stdout and stderr of the task will be sent) inputs (entire inputs will be
+        passed) or any input field name (a specific input field will be sent).
+    """
+    metadata = {
+        "help_string": help_string,
+        "mandatory": mandatory,
+        "output_file_template": output_file_template,
+        "output_field_name": output_field_name,
+        "keep_extension": keep_extension,
+        "requires": requires,
+        "callable": callable,
+    }
+
+    return attrs.field(metadata={k: v for k, v in metadata.items() if v is not None})
diff --git a/pydra/mark/tests/test_shell_commands.py b/pydra/mark/tests/test_shell_commands.py
@@ -0,0 +1,75 @@
+import os
+import tempfile
+from pathlib import Path
+import attrs
+import pydra.engine
+from pydra.mark import cmd_arg, cmd_out
+
+
+def test_shell_cmd():
+    @attrs.define(kw_only=True, slots=False)
+    class LsInputSpec(pydra.specs.ShellSpec):
+        directory: os.PathLike = cmd_arg(
+            help_string="the directory to list the contents of",
+            argstr="",
+            mandatory=True,
+        )
+        hidden: bool = cmd_arg(help_string=("display hidden FS objects"), argstr="-a")
+        long_format: bool = cmd_arg(
+            help_string=(
+                "display properties of FS object, such as permissions, size and timestamps "
+            ),
+            argstr="-l",
+        )
+        human_readable: bool = cmd_arg(
+            help_string="display file sizes in human readable form",
+            argstr="-h",
+            requires=["long_format"],
+        )
+        complete_date: bool = cmd_arg(
+            help_string="Show complete date in long format",
+            argstr="-T",
+            requires=["long_format"],
+            xor=["date_format_str"],
+        )
+        date_format_str: str = cmd_arg(
+            help_string="format string for ",
+            argstr="-D",
+            requires=["long_format"],
+            xor=["complete_date"],
+        )
+
+    def list_outputs(stdout):
+        return stdout.split("\n")[:-1]
+
+    @attrs.define(kw_only=True, slots=False)
+    class LsOutputSpec(pydra.specs.ShellOutSpec):
+        entries: list = cmd_out(
+            help_string="list of entries returned by ls command", callable=list_outputs
+        )
+
+    class Ls(pydra.engine.ShellCommandTask):
+        """Task definition for mri_aparc2aseg."""
+
+        executable = "ls"
+
+        input_spec = pydra.specs.SpecInfo(
+            name="LsInput",
+            bases=(LsInputSpec,),
+        )
+
+        output_spec = pydra.specs.SpecInfo(
+            name="LsOutput",
+            bases=(LsOutputSpec,),
+        )
+
+    tmpdir = Path(tempfile.mkdtemp())
+    Path.touch(tmpdir / "a")
+    Path.touch(tmpdir / "b")
+    Path.touch(tmpdir / "c")
+
+    ls = Ls(directory=tmpdir)
+
+    result = ls()
+
+    assert result.output.entries == ["a", "b", "c"]