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b/deduce/lookup_struct_loader.py |
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"""Some functions for creating lookup structures from raw items.""" |
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import docdeid as dd |
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from docdeid import Tokenizer |
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from deduce.str import FilterBasedOnLookupSet, TitleCase, UpperCase, UpperCaseFirstChar |
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from deduce.utils import lookup_set_to_trie |
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def load_common_word_lookup(raw_itemsets: dict[str, set[str]]) -> dd.ds.LookupSet: |
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"""Load common_word LookupSet.""" |
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common_word = dd.ds.LookupSet() |
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common_word.add_items_from_iterable( |
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raw_itemsets["common_word"], |
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) |
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surnames_lowercase = dd.ds.LookupSet() |
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surnames_lowercase.add_items_from_iterable( |
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raw_itemsets["surname"], |
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cleaning_pipeline=[ |
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dd.str.LowercaseString(), |
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dd.str.FilterByLength(min_len=2), |
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], |
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) |
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common_word -= surnames_lowercase |
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return common_word |
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def load_whitelist_lookup(raw_itemsets: dict[str, set[str]]) -> dd.ds.LookupSet: |
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""" |
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Load whitelist LookupSet. |
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Composed of medical terms, top 1000 frequent words (except surnames), and stopwords. |
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""" |
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medical_term = dd.ds.LookupSet() |
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medical_term.add_items_from_iterable( |
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raw_itemsets["medical_term"], |
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) |
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common_word = load_common_word_lookup(raw_itemsets) |
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stop_word = dd.ds.LookupSet() |
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stop_word.add_items_from_iterable(raw_itemsets["stop_word"]) |
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whitelist = dd.ds.LookupSet(matching_pipeline=[dd.str.LowercaseString()]) |
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whitelist.add_items_from_iterable( |
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medical_term + common_word + stop_word, |
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cleaning_pipeline=[dd.str.FilterByLength(min_len=2)], |
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) |
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return whitelist |
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def load_eponymous_disease_lookup( |
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raw_itemsets: dict[str, set[str]], tokenizer: Tokenizer |
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) -> dd.ds.LookupTrie: |
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"""Loads eponymous disease LookupTrie (e.g. Henoch-Schonlein).""" |
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epo_disease = dd.ds.LookupSet() |
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epo_disease.add_items_from_iterable(raw_itemsets["eponymous_disease"]) |
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epo_disease.add_items_from_self( |
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cleaning_pipeline=[dd.str.ReplaceNonAsciiCharacters()] |
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) |
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return lookup_set_to_trie(epo_disease, tokenizer) |
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def load_prefix_lookup(raw_itemsets: dict[str, set[str]]) -> dd.ds.LookupSet: |
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"""Load prefix LookupSet (e.g. 'dr', 'mw').""" |
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prefix = dd.ds.LookupSet() |
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prefix.add_items_from_iterable(raw_itemsets["prefix"]) |
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prefix.add_items_from_self(cleaning_pipeline=[UpperCaseFirstChar()]) |
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return prefix |
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def load_first_name_lookup( |
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raw_itemsets: dict[str, set[str]], tokenizer: Tokenizer |
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) -> dd.ds.LookupTrie: |
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"""Load first_name LookupTrie.""" |
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first_name = dd.ds.LookupSet() |
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first_name.add_items_from_iterable( |
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raw_itemsets["first_name"], |
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cleaning_pipeline=[dd.str.FilterByLength(min_len=2)], |
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) |
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first_name.add_items_from_self( |
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cleaning_pipeline=[ |
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FilterBasedOnLookupSet( |
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filter_set=load_whitelist_lookup(raw_itemsets), case_sensitive=False |
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), |
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], |
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replace=True, |
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) |
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return lookup_set_to_trie(first_name, tokenizer) |
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def load_interfix_lookup(raw_itemsets: dict[str, set[str]]) -> dd.ds.LookupSet: |
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"""Load interfix LookupSet ('van der', etc.).""" |
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interfix = dd.ds.LookupSet() |
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interfix.add_items_from_iterable(raw_itemsets["interfix"]) |
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interfix.add_items_from_self(cleaning_pipeline=[UpperCaseFirstChar()]) |
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interfix.add_items_from_self(cleaning_pipeline=[TitleCase()]) |
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interfix.remove_items_from_iterable(["V."]) |
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return interfix |
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def load_surname_lookup( |
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raw_itemsets: dict[str, set[str]], tokenizer: Tokenizer |
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) -> dd.ds.LookupTrie: |
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"""Load surname LookupTrie.""" |
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surname = dd.ds.LookupSet() |
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surname.add_items_from_iterable( |
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raw_itemsets["surname"], |
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cleaning_pipeline=[dd.str.FilterByLength(min_len=2)], |
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) |
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surname.add_items_from_self( |
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cleaning_pipeline=[ |
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FilterBasedOnLookupSet( |
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filter_set=load_whitelist_lookup(raw_itemsets), case_sensitive=False |
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), |
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], |
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replace=True, |
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) |
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return lookup_set_to_trie(surname, tokenizer) |
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def load_street_lookup( |
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raw_itemsets: dict[str, set[str]], tokenizer: Tokenizer |
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) -> dd.ds.LookupTrie: |
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"""Load street LookupTrie.""" |
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street = dd.ds.LookupSet() |
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street.add_items_from_iterable( |
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raw_itemsets["street"], |
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cleaning_pipeline=[ |
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dd.str.StripString(), |
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dd.str.FilterByLength(min_len=4), |
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], |
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) |
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street.add_items_from_self(cleaning_pipeline=[dd.str.ReplaceNonAsciiCharacters()]) |
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return lookup_set_to_trie(street, tokenizer) |
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def load_placename_lookup( |
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raw_itemsets: dict[str, set[str]], tokenizer: Tokenizer |
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) -> dd.ds.LookupTrie: |
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"""Load placename LookupTrie.""" |
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placename = dd.ds.LookupSet() |
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placename.add_items_from_iterable( |
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raw_itemsets["placename"], |
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cleaning_pipeline=[ |
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dd.str.StripString(), |
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], |
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) |
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placename.add_items_from_self( |
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cleaning_pipeline=[dd.str.ReplaceNonAsciiCharacters()] |
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) |
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placename.add_items_from_self( |
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cleaning_pipeline=[ |
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dd.str.ReplaceValue("(", ""), |
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dd.str.ReplaceValue(")", ""), |
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dd.str.ReplaceValue(" ", " "), |
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] |
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) |
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placename.add_items_from_self(cleaning_pipeline=[UpperCase()]) |
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placename.add_items_from_self( |
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cleaning_pipeline=[ |
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FilterBasedOnLookupSet( |
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filter_set=load_whitelist_lookup(raw_itemsets), case_sensitive=False |
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), |
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], |
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replace=True, |
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) |
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return lookup_set_to_trie(placename, tokenizer) |
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def load_hospital_lookup( |
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raw_itemsets: dict[str, set[str]], tokenizer: Tokenizer |
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) -> dd.ds.LookupTrie: |
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"""Load hopsital LookupTrie.""" |
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hospital = dd.ds.LookupSet(matching_pipeline=[dd.str.LowercaseString()]) |
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hospital.add_items_from_iterable(raw_itemsets["hospital"]) |
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hospital.add_items_from_iterable(raw_itemsets["hospital_abbr"]) |
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hospital.add_items_from_self( |
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cleaning_pipeline=[dd.str.ReplaceNonAsciiCharacters()], |
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) |
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return lookup_set_to_trie(hospital, tokenizer) |
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def load_institution_lookup( |
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raw_itemsets: dict[str, set[str]], tokenizer: Tokenizer |
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) -> dd.ds.LookupTrie: |
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"""Load institution LookupTrie.""" |
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institution = dd.ds.LookupSet() |
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institution.add_items_from_iterable( |
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raw_itemsets["healthcare_institution"], |
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cleaning_pipeline=[dd.str.StripString(), dd.str.FilterByLength(min_len=4)], |
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) |
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institution.add_items_from_self(cleaning_pipeline=[UpperCase()]) |
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institution.add_items_from_self( |
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cleaning_pipeline=[dd.str.ReplaceNonAsciiCharacters()], |
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) |
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institution = institution - load_whitelist_lookup(raw_itemsets) |
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return lookup_set_to_trie(institution, tokenizer) |