<commit_before>import logging
import xml.etree.ElementTree as ET
from dipper.sources.Source import Source
from dipper.models.assoc.G2PAssoc import G2PAssoc
from dipper.models.Genotype import Genotype
from dipper.models.Model import Model

LOG = logging.getLogger(__name__)


class Orphanet(Source):
    """
    Orphanet’s aim is to help improve the diagnosis,
    care and treatment of patients with rare diseases.
    For Orphanet, we are currently only parsing the disease-gene associations.
    """

    files = {
        'disease-gene': {
            'file': 'en_product6.xml',
            'url': 'http://www.orphadata.org/data/xml/en_product6.xml'}
    }

    def __init__(self, graph_type, are_bnodes_skolemized):
        super().__init__(
            graph_type,
            are_bnodes_skolemized,
            'orphanet',
            ingest_title='Orphanet',
            ingest_url='http://www.orpha.net',
            license_url=None,<commit_msg>added back snippet of possibly useful commented-out code that I perhaps overzealously nuked<commit_after>import logging
import xml.etree.ElementTree as ET
from dipper.sources.Source import Source
from dipper.models.assoc.G2PAssoc import G2PAssoc
from dipper.models.Genotype import Genotype
from dipper.models.Model import Model

LOG = logging.getLogger(__name__)


class Orphanet(Source):
    """
    Orphanet’s aim is to help improve the diagnosis,
    care and treatment of patients with rare diseases.
    For Orphanet, we are currently only parsing the disease-gene associations.
    """

    """ 
    Some useful code:
    xmlstarlet sel -t  -v "/JDBOR/DisorderList/Disorder/DisorderGeneAssociationList/
    """
    
    files = {
        'disease-gene': {
            'file': 'en_product6.xml',
            'url': 'http://www.orphadata.org/data/xml/en_product6.xml'}
    }

    def __init__(self, graph_type, are_bnodes_skolemized):
        super().__init__(
            graph_type,
            are_bnodes_skolemized,
            'orphanet',
            ingest_title='Orphanet',
            ingest_url='http://www.orpha.net',
            license_url=None,
{'fraction_non_alphanumeric': 0.09456264775413711, 'fraction_numerical': 0.0037825059101654845, 'mean_word_length': 2.7651245551601424, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 9}, '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': '5493970', 'n_tokens_mistral': 659, 'n_tokens_neox': 638, 'n_words': 157}