From 6c20227159ef29cbdc113128dcb84cdefa7cd2b0 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Sat, 4 Apr 2020 15:45:23 +0100
Subject: [PATCH] update to phase calculator runner to produce summary of phase
information from VLE calculation.
---
.../runners/phasecalculatorrunner.py | 31 +++++++++--
.../runnerstest/phasecalculatorrunnertest.py | 53 +++++++++++++------
2 files changed, 62 insertions(+), 22 deletions(-)
diff --git a/phasecalculator/runners/phasecalculatorrunner.py b/phasecalculator/runners/phasecalculatorrunner.py
index 8b6d61d..356260f 100755
--- a/phasecalculator/runners/phasecalculatorrunner.py
+++ b/phasecalculator/runners/phasecalculatorrunner.py
@@ -188,9 +188,12 @@ def run_vle_analysis(system_info, phase_filename, **kwargs):
"""
jar_path = system_info.runtime_information.phasetransfer_jar
- output_filename = create_phase_output_filename(phase_filename)
- return vlerun.run_vle_calculation(
- jar_path, phase_filename, output_filename, **kwargs
+ phase_output_filename = create_phase_output_filename(phase_filename)
+ csv_filename = create_phase_summary_filename(system_info.runtime_information.output_dir,
+ phase_filename)
+ vlerun.calculate_and_process_vle_data(
+ jar_path, phase_filename, phase_output_filename,
+ csv_filename, **kwargs
)
@@ -211,9 +214,27 @@ def create_output_dir(system_info):
output_path.mkdir(parents=True, exist_ok=True)
return output_path.as_posix()
+def create_phase_summary_filename(output_dir, phase_filename):
+ """Create phase summary CSV filename.
+
+ Parameters
+ ----------
+ output_dir : str
+ output directory name.
+ phase_filename : str
+ phase filename.
+
+ Returns
+ -------
+ str
+ CSV filename.
+
+ """
+ summary_filename = phase_filename.split("/")[-1].replace(".xml", "calculation_summary.csv")
+ return (pathlib.Path(output_dir) /summary_filename).as_posix()
def create_free_energy_output_filename(solvent_filename):
- """Create free energy filename for solvent file.
+ """Create free energy filename for solvent file.
Parameters
----------
@@ -263,7 +284,7 @@ def create_fractional_occupancy_filename(solvent_filename):
return solvent_filename.replace(".xml", "_fracocc.xml")
def create_phase_output_filename(phase_filename):
- """
+ """Create phase output filename.
Parameters
----------
diff --git a/phasecalculator/test/runnerstest/phasecalculatorrunnertest.py b/phasecalculator/test/runnerstest/phasecalculatorrunnertest.py
index a8338b1..ba1e808 100755
--- a/phasecalculator/test/runnerstest/phasecalculatorrunnertest.py
+++ b/phasecalculator/test/runnerstest/phasecalculatorrunnertest.py
@@ -109,7 +109,19 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
.absolute()
.as_posix()
)
+ self.expected_phase_output_filename = (
+ (parent_directory / "resources" / "expected_phasecalculated.xml")
+ .absolute()
+ .as_posix()
+ )
+ self.expected_phas_csv = (
+ (parent_directory / "resources" / "expected_phasesummary.csv")
+ .absolute()
+ .as_posix()
+ )
self.phase_filename = "scratch/systemphase.xml"
+ self.phase_out_file = "scratch/systemphasecalculated.xml"
+ self.output_csv_file = "fgip/systemphasecalculation_summary.csv"
self.solv_energy_dict = {
"solvent_filename": self.expected_solvent_file,
"temperature_value": 298.0,
@@ -166,7 +178,7 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
)
shutil.copyfile(self.expected_free_file, "scratch/systemsolvent_298.0Kfree.xml")
shutil.copyfile(self.frac_occ_filename, "scratch/systemsolvent_298.0K_fracocc.xml")
-
+ shutil.copyfile(self.expected_phase_output_filename, self.phase_out_file)
def test_run_all_analysis(self):
"""Test
@@ -181,6 +193,12 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
self.assertTrue(pathlib.Path(self.solvent_map).is_file())
self.assertTrue(pathlib.Path(self.fgip_file).is_file())
self.assertTrue(pathlib.Path(self.similarity_file).is_file())
+ with open(self.output_csv_file, "r") as act_file:
+ actual_contents = act_file.read()
+ with open(self.expected_phas_csv, "r") as exp_file:
+ expected_contents = exp_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
+
def test_run_fgip_analysis(self):
"""Test
@@ -218,22 +236,12 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
None.
"""
- expected_args = [
- "java",
- "-jar",
- self.example_jar,
- "--phaseOut",
- "--phaseCollectionList",
- "--conccalc",
- "--gascalc",
- "--calc",
- "--phaseFile",
- self.phase_filename,
- "-o",
- self.phase_filename.replace(".xml", "calculated.xml"),
- ]
- process = pcalcrun.run_vle_analysis(self.system, self.phase_filename)
- self.assertListEqual(expected_args, process.args)
+ pcalcrun.run_vle_analysis(self.system, self.phase_filename)
+ with open(self.output_csv_file, "r") as act_file:
+ actual_contents = act_file.read()
+ with open(self.expected_phas_csv, "r") as exp_file:
+ expected_contents = exp_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
def test_create_output_dir(self):
"""Test expected output directory created.
@@ -247,6 +255,17 @@ class PhaseCalculatorRunnerTestCase(unittest.TestCase):
pathlib.Path(self.system.runtime_information.output_dir).is_dir()
)
+ def test_create_phase_summary_filename(self):
+ """Test create phase summary filename.
+
+ Returns
+ -------
+ None.
+
+ """
+ expected_filename = "output/systemphasecalculation_summary.csv"
+ actual_filename = pcalcrun.create_phase_summary_filename("output", "scratch/systemphase.xml")
+ self.assertEqual(expected_filename, actual_filename)
def test_create_free_energy_output_filename(self):
"""Test expected filename produced.
--
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