Index

A

abstract_as_str() (scrapemed.paper.Paper method) add_paper() (scrapemed.paperSet.paperSet method)

add_papers() (scrapemed.paperSet.paperSet method) add_pmcid() (scrapemed.paperSet.paperSet method) add_pmcids() (scrapemed.paperSet.paperSet method)

B

badTextFormattingWarning

basicBiMap (class in scrapemed.utils) body_as_str() (scrapemed.paper.Paper method)

C

clean_xml_string() (in module scrapemed._clean)

cleanerdoc() (in module scrapemed.utils)

D

define_data_dict() (in module scrapemed._parse)

E

emptyTextWarning

expanded_query() (scrapemed.paper.Paper method)

F

from_pmc() (scrapemed.paper.Paper class method) from_pmcid_list() (scrapemed.paperSet.paperSet class method)

from_search() (scrapemed.paperSet.paperSet class method) from_xml() (scrapemed.paper.Paper class method) full_text() (scrapemed.paper.Paper method)

G

gather_abstract() (in module scrapemed._parse) gather_acknowledgements() (in module scrapemed._parse) gather_article_categories() (in module scrapemed._parse) gather_article_id() (in module scrapemed._parse) gather_article_types() (in module scrapemed._parse) gather_authors() (in module scrapemed._parse) gather_body() (in module scrapemed._parse) gather_custom_metadata() (in module scrapemed._parse) gather_footnote() (in module scrapemed._parse) gather_fpage() (in module scrapemed._parse) gather_funding() (in module scrapemed._parse) gather_issn() (in module scrapemed._parse) gather_issue() (in module scrapemed._parse) gather_journal_id() (in module scrapemed._parse) gather_journal_title() (in module scrapemed._parse) gather_lpage() (in module scrapemed._parse)

gather_non_author_contributors() (in module scrapemed._parse) gather_notes() (in module scrapemed._parse) gather_permissions() (in module scrapemed._parse) gather_published_date() (in module scrapemed._parse) gather_publisher_location() (in module scrapemed._parse) gather_publisher_name() (in module scrapemed._parse) gather_title() (in module scrapemed._parse) gather_volume() (in module scrapemed._parse) generate_mhtml_tag() (in module scrapemed._morehtml) generate_paper_dict() (in module scrapemed._parse) generate_typed_mhtml_tag() (in module scrapemed._morehtml) get_ref_map() (scrapemed._text.TextElement method) get_section_text() (scrapemed._text.TextSection method) get_section_text_with_refs() (scrapemed._text.TextSection method) get_xml() (in module scrapemed.scrape) get_xmls() (in module scrapemed.scrape)

I

info() (scrapemed.paper.Paper method)

investigate_xml_tree() (in module scrapemed.trees)

M

module scrapemed scrapemed._clean scrapemed._morehtml scrapemed._parse scrapemed._text scrapemed._validate scrapemed.paper scrapemed.paperSet scrapemed.scrape scrapemed.trees scrapemed.utils

multipleTitleWarning

N

noDTDFoundError

P

Paper (class in scrapemed.paper) paper_dict_from_pmc() (in module scrapemed._parse) paperSet (class in scrapemed.paperSet)

print_abstract() (scrapemed.paper.Paper method) print_body() (scrapemed.paper.Paper method) pubmedHTTPError

Q

query() (scrapemed.paper.Paper method)

R

readHTMLFailure

remove_mhtml_tags() (in module scrapemed._morehtml) reversedBiMapComparisonWarning

S

scrapemed module scrapemed._clean module scrapemed._morehtml module scrapemed._parse module scrapemed._text module scrapemed._validate module scrapemed.paper module

scrapemed.paperSet module scrapemed.scrape module scrapemed.trees module scrapemed.utils module search_pmc() (in module scrapemed.scrape) set_ref_map() (scrapemed._text.TextElement method) split_text_and_refs() (in module scrapemed._clean) stringify_children() (in module scrapemed._text) stringify_note() (in module scrapemed._parse)

T

TextElement (class in scrapemed._text) TextFigure (class in scrapemed._text) TextParagraph (class in scrapemed._text)

TextSection (class in scrapemed._text) TextTable (class in scrapemed._text) to_df() (scrapemed.paperSet.paperSet method) to_relational() (scrapemed.paper.Paper method)

U

unescape_except() (in module scrapemed._morehtml) unexpectedMultipleMatchWarning unexpectedTagWarning unexpectedZeroMatchWarning

unhandledTextTagWarning unmatchedCitationWarning unmatchedFigureWarning unmatchedTableWarning

V

validate_xml() (in module scrapemed._validate) validationWarning vectorize() (scrapemed.paper.Paper method)

visualize() (scrapemed.paperSet.paperSet method) visualize_element_tree() (in module scrapemed.trees) visualize_title_wordcloud() (scrapemed.paperSet.paperSet method) visualize_unique_values() (scrapemed.paperSet.paperSet method)

X

xml_tree_from_string() (in module scrapemed.scrape)