Initial commit

example.py

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+
+import json
+
+from text2chem.regex_parser import RegExParser
+from text2chem.parser_pipeline import ParserPipelineBuilder
+from text2chem.preprocessing_tools.additives_processing import AdditivesProcessing
+from text2chem.preprocessing_tools.chemical_name_processing import ChemicalNameProcessing
+from text2chem.preprocessing_tools.mixture_processing import MixtureProcessing
+from text2chem.preprocessing_tools.phase_processing import PhaseProcessing
+from text2chem.postprocessing_tools.substitute_additives import SubstituteAdditives
+
+
+mp = ParserPipelineBuilder() \
+    .add_preprocessing(AdditivesProcessing) \
+    .add_preprocessing(ChemicalNameProcessing) \
+    .add_preprocessing(PhaseProcessing) \
+    .add_preprocessing(MixtureProcessing)\
+    .add_postprocessing(SubstituteAdditives)\
+    .set_regex_parser(RegExParser)\
+    .build()
+
+
+def run_test(testdata):
+    for data in testdata:
+        chem_name = data["material"]
+        output = data["parser_output"][0]
+        result = mp.parse(chem_name).to_dict()
+        if output != result:
+            print(chem_name)
+
+"""
+test formulas
+"""
+testdata_fn = "tests/formulas.json"
+testdata = json.loads(open(testdata_fn).read())
+run_test(testdata)
+
+"""
+test additives
+"""
+testdata_fn = "tests/additives.json"
+testdata = json.loads(open(testdata_fn).read())
+run_test(testdata)
+
+"""
+test chemical names
+"""
+testdata_fn = "tests/chemical_names.json"
+testdata = json.loads(open(testdata_fn).read())
+run_test(testdata)
+
+"""
+test mixtures: alloys, solid solutions, composites
+"""
+testdata_fn = "tests/mixtures.json"
+testdata = json.loads(open(testdata_fn).read())
+run_test(testdata)
+
+"""
+test phases
+"""
+testdata_fn = "tests/phases.json"
+testdata = json.loads(open(testdata_fn).read())
+run_test(testdata)

requirements.txt

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+regex
+pubchempy
+sympy

setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name='text2chem',
+    packages=find_packages(),
+    version='0.0.1',
+    author='Ceder Research Group',
+    author_email='cedergroup-ml-team@lbl.gov',
+    description='RegEx-based text parser that converts chemical terms and material entities into chemical datastructure.',
+    zip_safe=False,
+    install_requires=[
+        "regex",
+        "pubchempy",
+        "sympy"
+    ],
+    include_package_data=True
+)