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refactor check_linear_fit #154

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refactor check_linear_fit #154

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2 changes: 1 addition & 1 deletion utils/fitting/check-linear-fit-tool/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# docker build -f Dockerfile -t mrbrandonwalker/check_linear_fit .
# docker build -f Dockerfile -t polusai/check-linear-fit-tool .
FROM condaforge/mambaforge

ENV EXEC_DIR="/opt/executables"
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15 changes: 7 additions & 8 deletions utils/fitting/check-linear-fit-tool/README.md
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Expand Up @@ -4,14 +4,13 @@ check_linear_fit

## Options

This plugin takes 6 input arguments and 1 output argument:
This plugin takes 5 input arguments and 1 output argument:

| Name | Description | I/O | Type | Default |
|---------------|-------------------------|--------|--------|---------|
| script | | Input | string | string |
| xs | | Input | {'type': 'array', 'items': 'float'} | {'type': 'array', 'items': 'float'} |
| ys | | Input | {'type': 'array', 'items': 'float'} | {'type': 'array', 'items': 'float'} |
| tol_quad | | Input | float | float |
| slope_min | | Input | float | float |
| slope_max | | Input | float | float |
| success | | Output | boolean | boolean |
| xs | x-axis input array | Input | {'type': 'array', 'items': 'float'} | {'type': 'array', 'items': 'float'} |
| ys | y-axis input array | Input | {'type': 'array', 'items': 'float'} | {'type': 'array', 'items': 'float'} |
| tol_quad | Quadratic tolerance term for determining if fit is linear | Input | float | float |
| slope_min | Min slope cut off | Input | float | float |
| slope_max | Max slope cut off | Input | float | float |
| success | Whether fit was successful or not | Output | boolean | boolean |
2 changes: 1 addition & 1 deletion ...heck-linear-fit-tool/check_linear_fit.cwl → ...inear-fit-tool/check_linear_fit_0@[email protected]
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Expand Up @@ -12,7 +12,7 @@ baseCommand: ["python", "-m", "polus.mm.utils.check_linear_fit"]

requirements:
DockerRequirement:
dockerPull: mrbrandonwalker/check_linear_fit
dockerPull: polusai/check-linear-fit-tool@sha256:20c3056601a244cfde2878cfe04ffc210ee7de6062065cbefe2a8fa0a69d4a0e
InlineJavascriptRequirement: {}

inputs:
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4 changes: 2 additions & 2 deletions utils/fitting/check-linear-fit-tool/ict.yml
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Expand Up @@ -5,8 +5,8 @@ container: check-linear-fit-tool
entrypoint:
title: check_linear_fit
description: check_linear_fit
author: Data Scientist
contact: [email protected]
author: Brandon Walker, Nazanin Donyapour
contact: [email protected], [email protected]
repository:
documentation:
citation:
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44 changes: 23 additions & 21 deletions utils/fitting/check-linear-fit-tool/tests/test_check_linear_fit.py
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@@ -1,16 +1,9 @@
"""Tests for check_linear_fit."""
import sys
from pathlib import Path

from polus.mm.utils.check_linear_fit.check_linear_fit import check_linear_fit

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
from sophios.api.pythonapi import Step
from sophios.api.pythonapi import Workflow


def test_check_linear_fit() -> None:
Expand Down Expand Up @@ -38,20 +31,29 @@ def test_check_linear_fit_out_of_bounds() -> None:

def test_check_linear_fit_cwl() -> None:
"""Test check_linear_fit CWL."""
# Define the input parameters
xs = [1.0, 2.0, 3.0]
ys = [1.0, 2.0, 3.0]
tol_quad = 0.1
slope_min = 0.5
slope_max = 1.5
cwl_file = Path("check_linear_fit.cwl")
input_to_props = parse_cwl_arguments(cwl_file)
input_to_props["xs"] = xs
input_to_props["ys"] = ys
input_to_props["tol_quad"] = tol_quad
input_to_props["slope_min"] = slope_min
input_to_props["slope_max"] = slope_max

input_yaml_path = Path("check_linear_fit-sfct.yml")
create_input_yaml(input_to_props, input_yaml_path)
stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
assert "success" in stdout

# Define paths
cwl_file_str = "check_linear_fit_0@[email protected]"
cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)

# Create the CWL step
check_linear_fit_step = Step(clt_path=cwl_file)
check_linear_fit_step.xs = xs
check_linear_fit_step.ys = ys
check_linear_fit_step.tol_quad = tol_quad
check_linear_fit_step.slope_min = slope_min
check_linear_fit_step.slope_max = slope_max

# Create the workflow and run it
steps = [check_linear_fit_step]
filename = "check_linear_fit_workflow"
workflow = Workflow(steps, filename)
workflow.run()

# cant check output because it is a boolean and no way to capture stdout
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