metapub

• metapub package
  • Subpackages
    • metapub.findit package
      • Subpackages
      • Submodules
      • metapub.findit.dances module
      • metapub.findit.findit module
      • metapub.findit.logic module
    • metapub.urlreverse package
      • Submodules
      • metapub.urlreverse.hostname2doiprefix module
      • metapub.urlreverse.hostname2jrnl module
      • metapub.urlreverse.methods module
      • metapub.urlreverse.urlreverse module
  • Submodules
  • metapub.base module
    • parse_elink_response()
    • MetaPubObject
      • MetaPubObject.__init__()
      • MetaPubObject.parse_xml()
    • Borg
      • Borg.__init__()
  • metapub.cache_utils module
    • datetime_to_timestamp()
    • get_cache_path()
    • cleanup_dir()
  • metapub.cite module
    • author_str()
    • citation()
    • article()
    • book()
    • bibtex()
  • metapub.clinvarfetcher module
    • ClinVarFetcher
      • ClinVarFetcher.__init__()
  • metapub.clinvarvariant module
    • PathogenicSummary
      • PathogenicSummary.counts
      • PathogenicSummary.total_submitters
      • PathogenicSummary.consensus
      • PathogenicSummary.conflicting
      • PathogenicSummary.review_status
      • PathogenicSummary.__init__()
    • ClinVarVariant
      • ClinVarVariant.__init__()
      • ClinVarVariant.to_dict()
      • ClinVarVariant.hgvs_c
      • ClinVarVariant.hgvs_g
      • ClinVarVariant.hgvs_p
      • ClinVarVariant.parse_xml()
  • metapub.config module
    • get_process_log()
    • get_data_log()
  • metapub.convert module
    • interpret_pmids_for_citation_results()
    • PubMedArticle2doi()
    • pmid2doi()
    • doi2pmid()
    • bookid2pmid()
    • main()
  • metapub.crossref module
    • get_most_similar_work_from_crossref_results()
    • CrossRefWork
      • CrossRefWork.__init__()
      • CrossRefWork.first_page
      • CrossRefWork.citation
      • CrossRefWork.pubyear
      • CrossRefWork.pubmonth
      • CrossRefWork.pubdate
      • CrossRefWork.author1
      • CrossRefWork.author1_last_fm
      • CrossRefWork.authors_str_lastfirst
      • CrossRefWork.author_list
      • CrossRefWork.author_list_last_fm
      • CrossRefWork.to_citation()
      • CrossRefWork.to_dict()
    • CrossRefFetcher
      • CrossRefFetcher.__init__()
      • CrossRefFetcher.article_by_doi()
      • CrossRefFetcher.article_by_pma()
      • CrossRefFetcher.article_by_title()
  • metapub.dx_doi module
    • DxDOI
      • DxDOI.resolve()
      • DxDOI.check_doi()
      • DxDOI.__init__()
      • DxDOI.check_doi()
      • DxDOI.resolve()
  • metapub.eutils_common module
    • get_eutils_client()
  • metapub.exceptions module
    • MetaPubError
      • MetaPubError.__init__()
      • MetaPubError.add_note()
      • MetaPubError.args
      • MetaPubError.with_traceback()
    • BaseXMLError
      • BaseXMLError.__init__()
      • BaseXMLError.add_note()
      • BaseXMLError.args
      • BaseXMLError.with_traceback()
    • InvalidPMID
      • InvalidPMID.__init__()
      • InvalidPMID.add_note()
      • InvalidPMID.args
      • InvalidPMID.with_traceback()
    • InvalidBookID
      • InvalidBookID.__init__()
      • InvalidBookID.add_note()
      • InvalidBookID.args
      • InvalidBookID.with_traceback()
    • CrossRefConnectionError
      • CrossRefConnectionError.__init__()
      • CrossRefConnectionError.add_note()
      • CrossRefConnectionError.args
      • CrossRefConnectionError.with_traceback()
    • NoPDFLink
      • NoPDFLink.__init__()
      • NoPDFLink.add_note()
      • NoPDFLink.args
      • NoPDFLink.with_traceback()
    • AccessDenied
      • AccessDenied.__init__()
      • AccessDenied.add_note()
      • AccessDenied.args
      • AccessDenied.with_traceback()
    • BadDOI
      • BadDOI.__init__()
      • BadDOI.add_note()
      • BadDOI.args
      • BadDOI.with_traceback()
    • DxDOIError
      • DxDOIError.__init__()
      • DxDOIError.add_note()
      • DxDOIError.args
      • DxDOIError.with_traceback()
  • metapub.medgenconcept module
    • MedGenConcept
      • MedGenConcept.__init__()
      • MedGenConcept.to_dict()
      • MedGenConcept.synonyms
      • MedGenConcept.medgen_uid
      • MedGenConcept.parse_xml()
  • metapub.medgenfetcher module
    • MedGenFetcher
      • MedGenFetcher.__init__()
  • metapub.ncbi_errors module
    • ServiceStatus
      • ServiceStatus.is_available
      • ServiceStatus.error_type
      • ServiceStatus.error_message
      • ServiceStatus.response_time
      • ServiceStatus.status_code
      • ServiceStatus.__init__()
    • NCBIErrorDetector
      • NCBIErrorDetector.__init__()
      • NCBIErrorDetector.check_service_status()
      • NCBIErrorDetector.diagnose_error()
    • check_ncbi_status()
    • diagnose_ncbi_error()
    • format_user_error()
    • NCBIServiceError
      • NCBIServiceError.__init__()
      • NCBIServiceError.add_note()
      • NCBIServiceError.args
      • NCBIServiceError.with_traceback()
    • handle_ncbi_request_error()
  • metapub.ncbi_health_check module
    • ServiceResult
      • ServiceResult.name
      • ServiceResult.url
      • ServiceResult.status
      • ServiceResult.response_time
      • ServiceResult.status_code
      • ServiceResult.error_message
      • ServiceResult.details
      • ServiceResult.__init__()
    • NCBIHealthChecker
      • NCBIHealthChecker.__init__()
      • NCBIHealthChecker.check_service()
      • NCBIHealthChecker.check_all_services()
    • print_status_icon()
    • print_results()
    • main()
  • metapub.pubmed_clinicalqueries module
  • metapub.pubmedarticle module
    • PubMedArticle
      • PubMedArticle.__init__()
      • PubMedArticle.to_dict()
      • PubMedArticle.citation
      • PubMedArticle.citation_html
      • PubMedArticle.citation_bibtex
      • PubMedArticle.pubdate
      • PubMedArticle.parse_xml()
    • square_voliss_data_for_pma()
    • determine_pubmed_xml_type()
  • metapub.pubmedauthor module
    • PubMedAuthor
      • PubMedAuthor.__init__()
      • PubMedAuthor.to_dict()
      • PubMedAuthor.parse_xml()
  • metapub.pubmedcentral module
    • get_pmid_for_otherid()
    • get_pmcid_for_otherid()
    • get_doi_for_otherid()
  • metapub.pubmedfetcher module
    • get_uids_from_esearch_result()
    • parse_related_pmids_result()
    • PubMedFetcher
      • PubMedFetcher.__init__()
      • PubMedFetcher.pmids_for_clinical_query()
      • PubMedFetcher.pmids_for_medical_genetics_query()
      • PubMedFetcher.pmids_for_citation()
      • PubMedFetcher.related_pmids()
      • PubMedFetcher.pmid_for_bookID()
  • metapub.pubmedfetcher_cli module
    • print_pma()
    • main()
  • metapub.text_mining module
    • findall_ncbi_bookIDs()
    • is_ncbi_bookID()
    • findall_pmcIDs()
    • is_pmcid()
    • pick_pmid()
    • findall_dois_in_text()
    • find_doi_in_string()
    • scrape_doi_from_article_page()
    • get_pmc_fulltext_filename_for_PubMedArticle()
  • metapub.utils module
    • kpick()
    • remove_chars()
    • hostname_of()
    • rootdomain_of()
    • asciify()
    • squash_spaces()
    • parameterize()
    • deparameterize()
    • remove_html_markup()
    • lowercase_keys()
  • metapub.validate module
    • assert_is_good_doi()
    • assert_is_good_pmid()