<commit_before>from belpy.biopax import biopax_api
from belpy.pysb_assembler import PysbAssembler

def test_hyphenated_agent_names():
    """This query should contain reactions with agent names RAF1-BRAF,
    which need to be canonicalized to Python-compatible names before
    model assembly."""
    bp = biopax_api.process_pc_neighborhood(['BRAF'])
    bp.get_phosphorylation()
    pa = PysbAssembler()
    pa.add_statements(bp.statements)
    pa.make_model()<commit_msg>Biopax autoclass tests<commit_after>from jnius import autoclass
from belpy.biopax import biopax_api
from belpy.pysb_assembler import PysbAssembler

def test_hyphenated_agent_names():
    """This query should contain reactions with agent names RAF1-BRAF,
    which need to be canonicalized to Python-compatible names before
    model assembly."""
    bp = biopax_api.process_pc_neighborhood(['BRAF'])
    bp.get_phosphorylation()
    pa = PysbAssembler()
    pa.add_statements(bp.statements)
    pa.make_model()

def test_paxtools_autoclass():
    autoclass('org.biopax.paxtools.impl.level3.ProteinImpl')

def test_biopaxpattern_autoclass():
    autoclass('org.biopax.paxtools.pattern.PatternBox')

def test_cpath_autoclass():
    autoclass('cpath.client.CPathClient')
{'fraction_non_alphanumeric': 0.08870967741935484, 'fraction_numerical': 0.0024193548387096775, 'mean_word_length': 5.083333333333333, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4522389', 'n_tokens_mistral': 434, 'n_tokens_neox': 410, 'n_words': 88}