array-indices (#67)

Co-authored-by: Brandon Duane Walker <[email protected]>

utils/array-indices-plugin/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/mm/utils/array_indices/__init__.py]

utils/array-indices-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/array-indices-plugin/.gitignore

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+poetry.lock

utils/array-indices-plugin/CHANGELOG.md

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+# CHANGELOG
+
+## 0.1.0
+
+Initial release.

utils/array-indices-plugin/README.md

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+# array_indices (0.1.0)
+
+return a subset from a array based on input indices
+
+## Options
+
+This plugin takes 2 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_indices | Indices to subset | Input | int[] | int[] |
+| input_array | Array to be make subset from | Input | Any | Any |
+| output_array | Path to the output array (subset) | Output | Any | Any |

utils/array-indices-plugin/VERSION

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+0.1.0

utils/array-indices-plugin/array_indices.cwl

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+
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+
+class: CommandLineTool
+
+label: return a subset from a array based on input indices
+
+doc: |-
+  This class return a subset from a array based on input indices
+baseCommand: "true"
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  input_indices:
+    label: input indices list
+    type: int[]
+
+  input_array:
+    label: Path to the input array
+    type: Any
+
+outputs:
+  output_array:
+    label: Path to the output array (subset)
+    doc: |-
+      Path to the output array (subset)
+    type: Any
+    outputBinding:
+      outputEval: |
+        ${
+          const data = [];
+          for (const index of inputs.input_indices) {
+            data.push(inputs.input_array[index]);
+          }
+          return data;
+        }
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/array-indices-plugin/ict.yml

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+specVersion: "0.1.0"
+name: array_indices
+version: 0.1.0
+container: array-indices-plugin
+entrypoint:
+title: array_indices
+description: return a subset from a array based on input indices
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: input_indices
+    required: true
+    description:
+    type: int[]
+  - name: input_array
+    required: true
+    description:
+    type: Any
+outputs:
+  - name: output_array
+    required: true
+    description: Path to the output array (subset)
+    type: Any
+ui:
+  - key: inputs.input_indices
+    title: "input_indices: "
+    description: ""
+    type: int[]
+  - key: inputs.input_array
+    title: "input_array: "
+    description: ""
+    type: Any

utils/array-indices-plugin/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-array-indices"
+version = "0.1.0"
+description = "return a subset from a array based on input indices"
+authors = ["Data Scientist <[email protected]>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+typer = "^0.7.0"
+cwl-utils = "0.33"
+cwltool = "3.1.20240404144621"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pytest = "^7.4"
+pytest-sugar = "^0.9.6"
+pre-commit = "^3.2.1"
+black = "^23.3.0"
+mypy = "^1.1.1"
+ruff = "^0.0.270"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]

utils/array-indices-plugin/tests/__init__.py

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+"""Tests for array_indices."""

utils/array-indices-plugin/tests/test_array_indices.py

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+"""Tests for array_indices."""
+import json
+import sys
+from pathlib import Path
+
+current_dir = Path(__file__).resolve().parent
+target_dir = current_dir.parent.parent.parent / "cwl_utils"
+sys.path.append(str(target_dir))
+
+from cwl_utilities import call_cwltool  # noqa: E402
+from cwl_utilities import create_input_yaml  # noqa: E402
+from cwl_utilities import parse_cwl_arguments  # noqa: E402
+
+
+def test_array_indices() -> None:
+    """Test array_indices."""
+    cwl_file = Path("array_indices.cwl")
+    input_to_props = parse_cwl_arguments(cwl_file)
+    input_to_props["input_indices"] = [1, 3]
+    input_to_props["input_array"] = [1, 2, 3, 4, 5]
+    input_yaml_path = Path("array_indices.yml")
+    create_input_yaml(input_to_props, input_yaml_path)
+    stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
+    output_data = json.loads(stdout)
+    output_array = output_data["output_array"]
+    assert output_array == [2, 4]