From 77d5556d9e3e28d8a1d57f2e2a8d787a6e8928a4 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Mon, 3 Feb 2020 14:43:24 +0000
Subject: [PATCH] ad methods to write SystemCollection to file. Update to
namespace and schema compliance.
Update to write lower case boolean expressions to conform to xsd:boolean type.
Update to schema namespace to: http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema
---
phasecalculator/classes/outputinformation.py | 17 +--
phasecalculator/classes/xmlnamespacing.py | 2 +-
.../io/systemcollectionprocessor.py | 71 ++++++++++
.../test/classestest/moleculetest.py | 2 +-
.../test/classestest/outputinformationtest.py | 14 +-
.../test/classestest/phasestest.py | 2 +-
phasecalculator/test/classestest/phasetest.py | 2 +-
.../classestest/runtimeinformationtest.py | 8 +-
.../test/classestest/systemtest.py | 16 +--
.../test/classestest/temperaturetest.py | 2 +-
.../iotest/systemcollectionprocessortest.py | 121 ++++++++++++++++++
11 files changed, 225 insertions(+), 32 deletions(-)
create mode 100755 phasecalculator/io/systemcollectionprocessor.py
create mode 100755 phasecalculator/test/iotest/systemcollectionprocessortest.py
diff --git a/phasecalculator/classes/outputinformation.py b/phasecalculator/classes/outputinformation.py
index f804851..c66313f 100755
--- a/phasecalculator/classes/outputinformation.py
+++ b/phasecalculator/classes/outputinformation.py
@@ -65,23 +65,24 @@ class OutputInformation(object):
@classmethod
def parse_fgip_output(cls, output_xml):
xpath_expression = "phasecalc:FGIPOutput/text()"
- fgip_output = bool(output_xml.xpath(xpath_expression, namespaces=PHASE_CALC_NAMESPACE_DICT)[0])
- return fgip_output
+ fgip_output = output_xml.xpath(xpath_expression, namespaces=PHASE_CALC_NAMESPACE_DICT)[0]
+ return True if fgip_output == "true" else False
@classmethod
def parse_similarity_output(cls, output_xml):
xpath_expression = "phasecalc:SimilarityOutput/text()"
- similarity_output = bool(output_xml.xpath(xpath_expression, namespaces=PHASE_CALC_NAMESPACE_DICT)[0])
+ similarity_output = output_xml.xpath(xpath_expression, namespaces=PHASE_CALC_NAMESPACE_DICT)[0]
if similarity_output:
type_xpath = "phasecalc:SimilarityOutput/@phasecalc:outputType"
similarity_output_type = output_xml.xpath(type_xpath, namespaces=PHASE_CALC_NAMESPACE_DICT)[0]
else:
similarity_output_type = None
+ similarity_output = True if similarity_output == "true" else False
return similarity_output, similarity_output_type
@classmethod
def parse_vle_output(cls, output_xml):
xpath_expression = "phasecalc:FGIPOutput/text()"
- vle_output = bool(output_xml.xpath(xpath_expression, namespaces=PHASE_CALC_NAMESPACE_DICT)[0])
- return vle_output
+ vle_output = output_xml.xpath(xpath_expression, namespaces=PHASE_CALC_NAMESPACE_DICT)[0]
+ return True if vle_output == "true" else False
def write_to_xml(self):
"""Write information to Etree representation of XML.
@@ -98,15 +99,15 @@ class OutputInformation(object):
return out_element
def write_fgip_output(self):
fgip_element = etree.Element(PHASE_CALCULATOR + "FGIPOutput", nsmap=PHASE_CALC_NAMESPACE_DICT)
- fgip_element.text = str(self.fgip_output)
+ fgip_element.text = str(self.fgip_output).lower()
return fgip_element
def write_similarity_output(self):
sim_element = etree.Element(PHASE_CALCULATOR + "SimilarityOutput", nsmap=PHASE_CALC_NAMESPACE_DICT)
- sim_element.text = str(self.similarity_output)
+ sim_element.text = str(self.similarity_output).lower()
if self.similarity_output_type is not None:
sim_element.set(PHASE_CALCULATOR + "outputType", self.similarity_output_type)
return sim_element
def write_vle_output(self):
vle_element = etree.Element(PHASE_CALCULATOR + "VLEOutput", nsmap=PHASE_CALC_NAMESPACE_DICT)
- vle_element.text = str(self.vle_output)
+ vle_element.text = str(self.vle_output).lower()
return vle_element
\ No newline at end of file
diff --git a/phasecalculator/classes/xmlnamespacing.py b/phasecalculator/classes/xmlnamespacing.py
index 6202a8d..82bfe41 100755
--- a/phasecalculator/classes/xmlnamespacing.py
+++ b/phasecalculator/classes/xmlnamespacing.py
@@ -26,6 +26,6 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-PHASE_CALC_NAMESPACE_DICT = {"phasecalc": "http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema"}
+PHASE_CALC_NAMESPACE_DICT = {"phasecalc": "http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema"}
PHASE_CALCULATOR = "{{{}}}".format(PHASE_CALC_NAMESPACE_DICT["phasecalc"])
diff --git a/phasecalculator/io/systemcollectionprocessor.py b/phasecalculator/io/systemcollectionprocessor.py
new file mode 100755
index 0000000..7084582
--- /dev/null
+++ b/phasecalculator/io/systemcollectionprocessor.py
@@ -0,0 +1,71 @@
+# -*- coding: utf-8 -*-
+# phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+# Copyright (C) 2019 Mark D. Driver
+#
+# phasecalculator is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+"""
+Script for IO handling of System Collection class.
+
+@author: Mark
+"""
+
+import logging
+from lxml import etree
+import xmlvalidator.xmlvalidation as xmlval
+from phasecalculator.classes.system import SystemCollection
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+
+def read_system_collection_file(xml_filename):
+ """Read SystemCollection from file.
+
+ Parameters
+ ----------
+ xml_filename : str
+ XML filename.
+
+ Returns
+ -------
+ SystemCollection
+ SystemCollection for calculations.
+
+ """
+ system_collection_etree = xmlval.validate_and_read_xml_file(xml_filename, xmlval.PHASE_CALCULATOR_SCHEMA)
+ return SystemCollection.parse_xml(system_collection_etree)
+
+
+def write_system_collection_file(system_collection, xml_filename):
+ """Write SystemCollection to XML file.
+
+ Parameters
+ ----------
+ system_collection : SystemCollection
+ SystemCollection for calculations.
+ xml_filename : str
+ XML filename.
+
+ Returns
+ -------
+ None.
+
+ """
+ sys_coll_element = system_collection.write_to_xml()
+ system_coll_etree = etree.ElementTree(sys_coll_element)
+ xmlval.validate_xml(system_coll_etree, xmlval.PHASE_CALCULATOR_SCHEMA)
+ system_coll_etree.write(
+ xml_filename, encoding="UTF-8", xml_declaration=True, pretty_print=True
+ )
\ No newline at end of file
diff --git a/phasecalculator/test/classestest/moleculetest.py b/phasecalculator/test/classestest/moleculetest.py
index de00d8b..10a71aa 100755
--- a/phasecalculator/test/classestest/moleculetest.py
+++ b/phasecalculator/test/classestest/moleculetest.py
@@ -67,7 +67,7 @@ class MoleculeTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:Molecule xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema" phasecalc:name="water" phasecalc:inChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phasecalc:ssipFileLocation="XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml" phasecalc:molefraction="1.0000"/>
+ expected_xml = """<phasecalc:Molecule xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema" phasecalc:name="water" phasecalc:inChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phasecalc:ssipFileLocation="XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml" phasecalc:molefraction="1.0000"/>
"""
actual_xml = self.molecule.write_to_xml()
self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
diff --git a/phasecalculator/test/classestest/outputinformationtest.py b/phasecalculator/test/classestest/outputinformationtest.py
index c8e27d6..7e93fcf 100755
--- a/phasecalculator/test/classestest/outputinformationtest.py
+++ b/phasecalculator/test/classestest/outputinformationtest.py
@@ -98,10 +98,10 @@ class OutputInformationTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:OutputInformation xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">
- <phasecalc:FGIPOutput>True</phasecalc:FGIPOutput>
- <phasecalc:SimilarityOutput phasecalc:outputType="all">True</phasecalc:SimilarityOutput>
- <phasecalc:VLEOutput>True</phasecalc:VLEOutput>
+ expected_xml = """<phasecalc:OutputInformation xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">
+ <phasecalc:FGIPOutput>true</phasecalc:FGIPOutput>
+ <phasecalc:SimilarityOutput phasecalc:outputType="all">true</phasecalc:SimilarityOutput>
+ <phasecalc:VLEOutput>true</phasecalc:VLEOutput>
</phasecalc:OutputInformation>
"""
actual_xml = self.out_inf.write_to_xml()
@@ -114,7 +114,7 @@ class OutputInformationTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:FGIPOutput xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">True</phasecalc:FGIPOutput>
+ expected_xml = """<phasecalc:FGIPOutput xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">true</phasecalc:FGIPOutput>
"""
actual_xml = self.out_inf.write_fgip_output()
self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
@@ -126,7 +126,7 @@ class OutputInformationTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:SimilarityOutput xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema" phasecalc:outputType="all">True</phasecalc:SimilarityOutput>
+ expected_xml = """<phasecalc:SimilarityOutput xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema" phasecalc:outputType="all">true</phasecalc:SimilarityOutput>
"""
actual_xml = self.out_inf.write_similarity_output()
self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
@@ -138,7 +138,7 @@ class OutputInformationTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:VLEOutput xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">True</phasecalc:VLEOutput>
+ expected_xml = """<phasecalc:VLEOutput xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">true</phasecalc:VLEOutput>
"""
actual_xml = self.out_inf.write_vle_output()
self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
diff --git a/phasecalculator/test/classestest/phasestest.py b/phasecalculator/test/classestest/phasestest.py
index 6b1f909..e088e48 100755
--- a/phasecalculator/test/classestest/phasestest.py
+++ b/phasecalculator/test/classestest/phasestest.py
@@ -76,7 +76,7 @@ class PhasesTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:Phases xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">
+ expected_xml = """<phasecalc:Phases xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">
<phasecalc:Phase>
<phasecalc:Molecule phasecalc:name="water" phasecalc:inChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phasecalc:ssipFileLocation="XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml" phasecalc:molefraction="1.0000"/>
<phasecalc:Temperature phasecalc:value="298.0" phasecalc:unit="KELVIN"/>
diff --git a/phasecalculator/test/classestest/phasetest.py b/phasecalculator/test/classestest/phasetest.py
index 0e28f72..3bd1764 100755
--- a/phasecalculator/test/classestest/phasetest.py
+++ b/phasecalculator/test/classestest/phasetest.py
@@ -93,7 +93,7 @@ class PhaseTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:Phase xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">
+ expected_xml = """<phasecalc:Phase xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">
<phasecalc:Molecule phasecalc:name="water" phasecalc:inChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phasecalc:ssipFileLocation="XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml" phasecalc:molefraction="1.0000"/>
<phasecalc:Temperature phasecalc:value="298.0" phasecalc:unit="KELVIN"/>
</phasecalc:Phase>
diff --git a/phasecalculator/test/classestest/runtimeinformationtest.py b/phasecalculator/test/classestest/runtimeinformationtest.py
index 10f3045..06f2e86 100755
--- a/phasecalculator/test/classestest/runtimeinformationtest.py
+++ b/phasecalculator/test/classestest/runtimeinformationtest.py
@@ -103,7 +103,7 @@ class RuntimeInformationTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:RuntimeInformation xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">
+ expected_xml = """<phasecalc:RuntimeInformation xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">
<phasecalc:PhaseTransferJar>resources/example.jar</phasecalc:PhaseTransferJar>
<phasecalc:ScratchDirectory>scratch</phasecalc:ScratchDirectory>
<phasecalc:OutputDirectory>fgip</phasecalc:OutputDirectory>
@@ -119,7 +119,7 @@ class RuntimeInformationTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:PhaseTransferJar xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">resources/example.jar</phasecalc:PhaseTransferJar>
+ expected_xml = """<phasecalc:PhaseTransferJar xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">resources/example.jar</phasecalc:PhaseTransferJar>
"""
actual_xml = self.runtime_inf.write_phasetransfer_jar_xml()
self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
@@ -131,7 +131,7 @@ class RuntimeInformationTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:ScratchDirectory xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">scratch</phasecalc:ScratchDirectory>
+ expected_xml = """<phasecalc:ScratchDirectory xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">scratch</phasecalc:ScratchDirectory>
"""
actual_xml = self.runtime_inf.write_scratch_dir_xml()
self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
@@ -143,7 +143,7 @@ class RuntimeInformationTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:OutputDirectory xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">fgip</phasecalc:OutputDirectory>
+ expected_xml = """<phasecalc:OutputDirectory xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">fgip</phasecalc:OutputDirectory>
"""
actual_xml = self.runtime_inf.write_output_dir_xml()
self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
\ No newline at end of file
diff --git a/phasecalculator/test/classestest/systemtest.py b/phasecalculator/test/classestest/systemtest.py
index 1c74366..ce47480 100755
--- a/phasecalculator/test/classestest/systemtest.py
+++ b/phasecalculator/test/classestest/systemtest.py
@@ -90,7 +90,7 @@ class SystemTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:SystemCollection xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">
+ expected_xml = """<phasecalc:SystemCollection xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">
<phasecalc:System>
<phasecalc:Phases>
<phasecalc:Phase>
@@ -104,9 +104,9 @@ class SystemTestCase(unittest.TestCase):
<phasecalc:OutputDirectory>fgip</phasecalc:OutputDirectory>
</phasecalc:RuntimeInformation>
<phasecalc:OutputInformation>
- <phasecalc:FGIPOutput>True</phasecalc:FGIPOutput>
- <phasecalc:SimilarityOutput phasecalc:outputType="all">True</phasecalc:SimilarityOutput>
- <phasecalc:VLEOutput>True</phasecalc:VLEOutput>
+ <phasecalc:FGIPOutput>true</phasecalc:FGIPOutput>
+ <phasecalc:SimilarityOutput phasecalc:outputType="all">true</phasecalc:SimilarityOutput>
+ <phasecalc:VLEOutput>true</phasecalc:VLEOutput>
</phasecalc:OutputInformation>
</phasecalc:System>
</phasecalc:SystemCollection>
@@ -131,7 +131,7 @@ class SystemTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:System xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema">
+ expected_xml = """<phasecalc:System xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">
<phasecalc:Phases>
<phasecalc:Phase>
<phasecalc:Molecule phasecalc:name="water" phasecalc:inChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phasecalc:ssipFileLocation="XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml" phasecalc:molefraction="1.0000"/>
@@ -144,9 +144,9 @@ class SystemTestCase(unittest.TestCase):
<phasecalc:OutputDirectory>fgip</phasecalc:OutputDirectory>
</phasecalc:RuntimeInformation>
<phasecalc:OutputInformation>
- <phasecalc:FGIPOutput>True</phasecalc:FGIPOutput>
- <phasecalc:SimilarityOutput phasecalc:outputType="all">True</phasecalc:SimilarityOutput>
- <phasecalc:VLEOutput>True</phasecalc:VLEOutput>
+ <phasecalc:FGIPOutput>true</phasecalc:FGIPOutput>
+ <phasecalc:SimilarityOutput phasecalc:outputType="all">true</phasecalc:SimilarityOutput>
+ <phasecalc:VLEOutput>true</phasecalc:VLEOutput>
</phasecalc:OutputInformation>
</phasecalc:System>
"""
diff --git a/phasecalculator/test/classestest/temperaturetest.py b/phasecalculator/test/classestest/temperaturetest.py
index 36b85c8..7effef7 100755
--- a/phasecalculator/test/classestest/temperaturetest.py
+++ b/phasecalculator/test/classestest/temperaturetest.py
@@ -67,7 +67,7 @@ class TemperatureTestCase(unittest.TestCase):
None.
"""
- expected_xml = """<phasecalc:Temperature xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema" phasecalc:value="298.0" phasecalc:unit="KELVIN"/>
+ expected_xml = """<phasecalc:Temperature xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema" phasecalc:value="298.0" phasecalc:unit="KELVIN"/>
"""
actual_xml = self.temperature.write_to_xml()
self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
diff --git a/phasecalculator/test/iotest/systemcollectionprocessortest.py b/phasecalculator/test/iotest/systemcollectionprocessortest.py
new file mode 100755
index 0000000..201380b
--- /dev/null
+++ b/phasecalculator/test/iotest/systemcollectionprocessortest.py
@@ -0,0 +1,121 @@
+# -*- coding: utf-8 -*-
+# phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+# Copyright (C) 2019 Mark D. Driver
+#
+# phasecalculator is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+"""
+Test case for System Collection Processor methods.
+
+@author: Mark
+"""
+
+import logging
+import unittest
+from lxml import etree
+from phasecalculator.classes.temperature import Temperature
+from phasecalculator.classes.molecule import Molecule
+from phasecalculator.classes.phase import Phase
+from phasecalculator.classes.phases import Phases
+from phasecalculator.classes.runtimeinformation import RuntimeInformation
+from phasecalculator.classes.outputinformation import OutputInformation
+from phasecalculator.classes.system import System, SystemCollection
+import phasecalculator.io.systemcollectionprocessor as sysproc
+
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class SystemCollectionProcessorTestCase(unittest.TestCase):
+ """Test case for System Collection Processor methods."""
+ def setUp(self):
+ """Set up before tests.
+
+ Returns
+ -------
+ None.
+
+ """
+ self.maxDiff = None
+ self.temperature = Temperature(298.0, "KELVIN")
+ self.molecule = Molecule("water", "XLYOFNOQVPJJNP-UHFFFAOYSA-N", "XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml", 1.0)
+ self.phase = Phase([self.molecule], self.temperature)
+ self.phases = Phases([self.phase])
+ self.example_jar = "resources/example.jar"
+ self.runtime_inf = RuntimeInformation(self.example_jar, "scratch", "fgip")
+ self.out_inf = OutputInformation(True, True, "all", True)
+ self.system = System(self.phases, self.runtime_inf, self.out_inf)
+ self.system_collection = SystemCollection([self.system])
+ self.xml_filename = "syscollection.xml"
+ sysproc.write_system_collection_file(self.system_collection, self.xml_filename)
+ def tearDown(self):
+ """Clean up after tests.
+
+ Returns
+ -------
+ None.
+
+ """
+ del self.phase
+ del self.molecule
+ del self.temperature
+ del self.phases
+ del self.runtime_inf
+ del self.out_inf
+ del self.system
+ del self.system_collection
+ def test_read_system_collection_file(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ actual_sys_collection = sysproc.read_system_collection_file(self.xml_filename)
+ self.assertEqual(self.system_collection, actual_sys_collection)
+ def test_write_system_collection_file(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ expected_contents = """<?xml version='1.0' encoding='UTF-8'?>
+<phasecalc:SystemCollection xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/PhaseCalculatorSchema">
+ <phasecalc:System>
+ <phasecalc:Phases>
+ <phasecalc:Phase>
+ <phasecalc:Molecule phasecalc:name="water" phasecalc:inChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phasecalc:ssipFileLocation="XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml" phasecalc:molefraction="1.0000"/>
+ <phasecalc:Temperature phasecalc:value="298.0" phasecalc:unit="KELVIN"/>
+ </phasecalc:Phase>
+ </phasecalc:Phases>
+ <phasecalc:RuntimeInformation>
+ <phasecalc:PhaseTransferJar>resources/example.jar</phasecalc:PhaseTransferJar>
+ <phasecalc:ScratchDirectory>scratch</phasecalc:ScratchDirectory>
+ <phasecalc:OutputDirectory>fgip</phasecalc:OutputDirectory>
+ </phasecalc:RuntimeInformation>
+ <phasecalc:OutputInformation>
+ <phasecalc:FGIPOutput>true</phasecalc:FGIPOutput>
+ <phasecalc:SimilarityOutput phasecalc:outputType="all">true</phasecalc:SimilarityOutput>
+ <phasecalc:VLEOutput>true</phasecalc:VLEOutput>
+ </phasecalc:OutputInformation>
+ </phasecalc:System>
+</phasecalc:SystemCollection>
+"""
+ with open(self.xml_filename, "r") as actual_file:
+ actual_contents = actual_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
+
--
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