import sys import json import sqlite3 import datetime import warnings from bs4 import BeautifulSoup from bs4.element import NavigableString import fatcat_client from .common import EntityImporter, clean, LANG_MAP_MARC # from: https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T.publication_types/?report=objectonly PUBMED_RELEASE_TYPE_MAP = { #Adaptive Clinical Trial "Address": "speech", "Autobiography": "book", #Bibliography "Biography": "book", #Case Reports "Classical Article": "article-journal", #Clinical Conference #Clinical Study #Clinical Trial #Clinical Trial, Phase I #Clinical Trial, Phase II #Clinical Trial, Phase III #Clinical Trial, Phase IV #Clinical Trial Protocol #Clinical Trial, Veterinary #Collected Works #Comparative Study #Congress #Consensus Development Conference #Consensus Development Conference, NIH #Controlled Clinical Trial "Dataset": "dataset", #Dictionary #Directory #Duplicate Publication "Editorial": "editorial", #English Abstract # doesn't indicate that this is abstract-only #Equivalence Trial #Evaluation Studies #Expression of Concern #Festschrift #Government Document #Guideline "Historical Article": "article-journal", #Interactive Tutorial "Interview": "interview", "Introductory Journal Article": "article-journal", "Journal Article": "article-journal", "Lecture": "speech", "Legal Case": "legal_case", "Legislation": "legislation", "Letter": "letter", #Meta-Analysis #Multicenter Study #News "Newspaper Article": "article-newspaper", #Observational Study #Observational Study, Veterinary #Overall #Patient Education Handout #Periodical Index #Personal Narrative #Portrait #Practice Guideline #Pragmatic Clinical Trial #Publication Components #Publication Formats #Publication Type Category #Randomized Controlled Trial #Research Support, American Recovery and Reinvestment Act #Research Support, N.I.H., Extramural #Research Support, N.I.H., Intramural #Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. #Research Support, U.S. Gov't, P.H.S. #Review # in the "literature review" sense, not "product review" #Scientific Integrity Review #Study Characteristics #Support of Research #Systematic Review "Technical Report": "report", #Twin Study #Validation Studies #Video-Audio Media #Webcasts } MONTH_ABBR_MAP = { "Jan": 1, "01": 1, "Feb": 2, "02": 2, "Mar": 3, "03": 3, "Apr": 4, "04": 4, "May": 5, "05": 5, "Jun": 6, "06": 6, "Jul": 7, "07": 7, "Aug": 8, "08": 8, "Sep": 9, "09": 9, "Oct": 10, "10": 10, "Nov": 11, "11": 11, "Dec": 12, "12": 12, } # From: https://www.ncbi.nlm.nih.gov/books/NBK7249/ COUNTRY_NAME_MAP = { "Afghanistan": "af", "Albania": "al", "Algeria": "dz", "Andorra": "ad", "Angola": "ao", "Antigua and Barbuda": "ag", "Argentina": "ar", "Armenia": "am", "Australia": "au", "Austria": "at", "Azerbaijan": "az", "Bahamas": "bs", "Bahrain": "bh", "Bangladesh": "bd", "Barbados": "bb", "Belarus": "by", "Belgium": "be", "Belize": "bz", "Benin": "bj", "Bhutan": "bt", "Bolivia": "bo", "Bosnia and Herzegowina": "ba", "Botswana": "bw", "Brazil": "br", "Brunei Darussalam": "bn", "Bulgaria": "bg", "Burkina Faso": "bf", "Burundi": "bi", "Cambodia": "kh", "Cameroon": "cm", "Canada": "ca", "Cape Verde": "cv", "Central African Republic": "cf", "Chad": "td", "Chile": "cl", "China": "cn", "Colombia": "co", "Comoros": "km", "Congo, Democratic Republic": "cd", "Congo, People’s Republic": "cg", "Costa Rica": "cr", "Cote d'Ivoire": "ci", "Croatia (Local Name: Hrvatska)": "hr", "Cuba": "cu", "Cyprus": "cy", "Czech Republic": "cz", "Denmark": "dk", "Djibouti": "dj", "Dominica": "dm", "Dominican Republic": "do", "East Timor": "tl", "Ecuador": "ec", "El Salvador": "sv", "Equatorial Guinea": "gq", "Eritrea": "er", "Estonia": "ee", "Ethiopia": "et", "Fiji": "fj", "Finland": "fi", "France": "fr", "Gabon": "ga", "Gambia": "gm", "Georgia": "ge", "Germany": "de", "Ghana": "gh", "Greece": "gr", "Greenland": "gl", "Grenada": "gd", "Guatemala": "gt", "Guinea": "gn", "Guinea-Bissau": "gw", "Guyana": "gy", "Haiti": "ht", "Honduras": "hn", "Hong Kong": "hk", "Hungary": "hu", "Iceland": "is", "India": "in", "Indonesia": "id", "Iran": "ir", "Iraq": "iq", "Ireland": "ie", "Israel": "il", "Italy": "it", "Jamaica": "jm", "Japan": "jp", "Jordan": "jo", "Kazakhstan": "kz", "Kenya": "ke", "Kiribati": "ki", "Korea, Democratic People's Republic": "kp", "Korea, Republic": "kr", "Kuwait": "kw", "Kyrgyzstan": "kg", "Laos": "la", "Latvia": "lv", "Lebanon": "lb", "Lesotho": "ls", "Liberia": "lr", "Libya": "ly", "Liechtenstein": "li", "Lithuania": "lt", "Luxembourg": "lu", "Macedonia": "mk", "Madagascar": "mg", "Malawi": "mw", "Malaysia": "my", "Maldives": "mv", "Mali": "ml", "Malta": "mt", "Marshall Islands": "mh", "Mauritania": "mr", "Mauritius": "mu", "Mexico": "mx", "Micronesia": "fm", "Moldova": "md", "Monaco": "mc", "Mongolia": "mn", "Morocco": "ma", "Mozambique": "mz", "Myanmar": "mm", "Namibia": "na", "Nauru": "nr", "Nepal": "np", "Netherlands": "nl", "New Zealand": "nz", "Nicaragua": "ni", "Niger": "ne", "Nigeria": "ng", "Norway": "no", "Oman": "om", "Pakistan": "pk", "Palau": "pw", "Panama": "pa", "Papua New Guinea": "pg", "Paraguay": "py", "Peru": "pe", "Philippines": "ph", "Poland": "pl", "Portugal": "pt", "Puerto Rico": "pr", "Qatar": "qa", "Romania": "ro", "Russian Federation": "ru", "Rwanda": "rw", "Saint Kitts and Nevis": "kn", "Saint Lucia": "lc", "Saint Vincent and the Grenadines": "vc", "Samoa": "ws", "San Marino": "sm", "Sao Tome and Príncipe": "st", "Saudi Arabia": "sa", "Senegal": "sn", "Serbia and Montenegro": "cs", "Seychelles": "sc", "Sierra Leone": "sl", "Singapore": "sg", "Slovakia (Slovak Republic)": "sk", "Slovenia": "si", "Solomon Islands": "sb", "Somalia": "so", "South Africa": "za", "Spain": "es", "Sri Lanka": "lk", "Sudan": "sd", "Suriname": "sr", "Swaziland": "sz", "Sweden": "se", "Switzerland": "ch", "Syrian Arab Republic": "sy", "Taiwan": "tw", "Tajikistan": "tj", "Tanzania": "tz", "Tanzania": "tz", "Thailand": "th", "Togo": "tg", "Tonga": "to", "Trinidad and Tobago": "tt", "Tunisia": "tn", "Turkey": "tr", "Turkmenistan": "tm", "Tuvalu": "tv", "Uganda": "ug", "Ukraine": "ua", "United Arab Emirates": "ae", "United Kingdom": "gb", "United States": "us", "Uruguay": "uy", # Additions from running over large files "Bosnia and Herzegovina": "ba", #"International" "China (Republic : 1949- )": "tw", # pretty sure this is tw not cn "Russia (Federation)": "ru", "Scotland": "gb", "England": "gb", "Korea (South)": "kr", "Georgia (Republic)": "ge", "Egypt": "eg", } class PubmedImporter(EntityImporter): """ Importer for PubMed/MEDLINE XML metadata. If lookup_refs is true, will do identifer-based lookups for all references. TODO: MEDLINE doesn't include PMC/OA license; could include in importer? """ def __init__(self, api, issn_map_file, lookup_refs=False, **kwargs): eg_desc = kwargs.get('editgroup_description', "Automated import of PubMed/MEDLINE XML metadata") eg_extra = kwargs.get('editgroup_extra', dict()) eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.PubmedImporter') super().__init__(api, issn_map_file=issn_map_file, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs) self.lookup_refs = lookup_refs extid_map_file = kwargs.get('extid_map_file') self.extid_map_db = None if extid_map_file: db_uri = "file:{}?mode=ro".format(extid_map_file) print("Using external ID map: {}".format(db_uri)) self.extid_map_db = sqlite3.connect(db_uri, uri=True) else: print("Not using external ID map") self.create_containers = kwargs.get('create_containers', True) self.read_issn_map_file(issn_map_file) def lookup_ext_ids(self, pmid): if self.extid_map_db is None: return dict(doi=None, core_id=None, pmid=None, pmcid=None, wikidata_qid=None, arxiv_id=None, jstor_id=None) row = self.extid_map_db.execute("SELECT core, doi, pmcid, wikidata FROM ids WHERE pmid=? LIMIT 1", [pmid]).fetchone() if row is None: return dict(doi=None, core_id=None, pmid=None, pmcid=None, wikidata_qid=None, arxiv_id=None, jstor_id=None) row = [str(cell or '') or None for cell in row] return dict( core_id=row[0], doi=row[1], pmcid=row[2], wikidata_qid=row[3], # TODO: arxiv_id=None, jstor_id=None, ) def want(self, obj): return True def parse_record(self, a): medline = a.MedlineCitation # PubmedData isn't required by DTD, but seems to always be present pubmed = a.PubmedData extra = dict() extra_pubmed = dict() identifiers = pubmed.ArticleIdList pmid = medline.PMID.string.strip() doi = identifiers.find("ArticleId", IdType="doi") if doi: doi = doi.string.lower() if doi.startswith('doi:'): doi = doi[4:] if not (doi.startswith('10.') and '/' in doi and doi.split('/')[1]): sys.stderr.write("BOGUS DOI: {}\n".format(doi)) doi = None pmcid = identifiers.find("ArticleId", IdType="pmc") if pmcid: pmcid = pmcid.string release_type = None pub_types = [] for pub_type in medline.Article.PublicationTypeList.find_all("PublicationType"): pub_types.append(pub_type.string) if pub_type.string in PUBMED_RELEASE_TYPE_MAP: release_type = PUBMED_RELEASE_TYPE_MAP[pub_type.string] break if pub_types: extra_pubmed['pub_types'] = pub_types if medline.Article.PublicationTypeList.find(string="Retraction of Publication"): release_type = "retraction" retraction_of = medline.find("CommentsCorrections", RefType="RetractionOf") if retraction_of: extra_pubmed['retraction_of_raw'] = retraction_of.RefSource.string extra_pubmed['retraction_of_pmid'] = retraction_of.PMID.string # everything in medline is published release_stage = "published" if medline.Article.PublicationTypeList.find(string="Corrected and Republished Article"): release_stage = "updated" if medline.Article.PublicationTypeList.find(string="Retraction of Publication"): release_stage = "retraction" withdrawn_status = None if medline.Article.PublicationTypeList.find(string="Retracted Publication"): withdrawn_status = "retracted" elif medline.find("CommentsCorrections", RefType="ExpressionOfConcernIn"): withdrawn_status = "concern" pages = medline.find('MedlinePgn') if pages: pages = pages.string title = medline.Article.ArticleTitle.string # always present if title: if title.endswith('.'): title = title[:-1] # this hides some "special" titles, but the vast majority are # translations; translations don't always include the original_title if title.startswith('[') and title.endswith(']'): title = title[1:-1] else: # will filter out later title = None original_title = medline.Article.find("VernacularTitle", recurse=False) if original_title: original_title = original_title.string or None if original_title and original_title.endswith('.'): original_title = original_title[:-1] # TODO: happening in alpha order, not handling multi-language well. language = medline.Article.Language if language: language = language.string if language in ("und", "un"): # "undetermined" language = None else: language = LANG_MAP_MARC.get(language) if not language: warnings.warn("MISSING MARC LANG: {}".format(medline.Article.Language.string)) ### Journal/Issue Metadata # MedlineJournalInfo is always present issnl = None container_id = None container_name = None container_extra = dict() mji = medline.MedlineJournalInfo if mji.find("Country"): country_name = mji.Country.string.strip() country_code = COUNTRY_NAME_MAP.get(country_name) if country_code: container_extra['country'] = country_code elif country_name: container_extra['country_name'] = country_name if mji.find("ISSNLinking"): issnl = mji.ISSNLinking.string journal = medline.Article.Journal issnp = journal.find("ISSN", IssnType="Print") if issnp: container_extra['issnp'] = issnp.string if not issnl: issnll = self.issn2issnl(issnp) if issnl: container_id = self.lookup_issnl(issnl) pub_date = medline.Article.find('ArticleDate') if not pub_date: pub_date = journal.PubDate release_date = None release_year = None if pub_date.Year: release_year = int(pub_date.Year.string) if pub_date.find("Day") and pub_date.find("Month"): release_date = datetime.date( release_year, MONTH_ABBR_MAP[pub_date.Month.string], int(pub_date.Day.string)) release_date = release_date.isoformat() if journal.find("Title"): container_name = journal.Title.string if (container_id is None and self.create_containers and (issnl is not None) and container_name): # name, type, publisher, issnl # extra: issnp, issne, original_name, languages, country ce = fatcat_client.ContainerEntity( name=container_name, container_type='journal', #NOTE: publisher not included issnl=issnl, extra=(container_extra or None)) ce_edit = self.create_container(ce) container_id = ce_edit.ident self._issnl_id_map[issnl] = container_id ji = journal.JournalIssue volume = None if ji.find("Volume"): volume = ji.Volume.string issue = None if ji.find("Issue"): issue = ji.Issue.string ### Abstracts # "All abstracts are in English" abstracts = [] primary_abstract = medline.find("Abstract") if primary_abstract and primary_abstract.AbstractText.get('NlmCategory'): joined = "\n".join([m.get_text() for m in primary_abstract.find_all("AbstractText")]) abst = fatcat_client.ReleaseAbstract( content=joined, mimetype="text/plain", lang="en", ) if abst.content: abstracts.append(abst) elif primary_abstract: for abstract in primary_abstract.find_all("AbstractText"): abst = fatcat_client.ReleaseAbstract( content=abstract.get_text().strip(), mimetype="text/plain", lang="en", ) if abst.content: abstracts.append(abst) if abstract.find('math'): abst = fatcat_client.ReleaseAbstract( # strip the tags content=str(abstract)[14:-15], mimetype="application/mathml+xml", lang="en", ) if abst.content: abstracts.append(abst) other_abstracts = medline.find_all("OtherAbstract") for other in other_abstracts: lang = "en" if other.get('Language'): lang = LANG_MAP_MARC.get(other['Language']) abst = fatcat_client.ReleaseAbstract( content=other.AbstractText.get_text().strip(), mimetype="text/plain", lang=lang, ) if abst.content: abstracts.append(abst) if not abstracts: abstracts = None ### Contribs contribs = [] if medline.AuthorList: for author in medline.AuthorList.find_all("Author"): creator_id = None given_name = None surname = None raw_name = None if author.ForeName: given_name = author.ForeName.string if author.LastName: surname = author.LastName.string if given_name and surname: raw_name = "{} {}".format(given_name, surname) elif surname: raw_name = surname if not raw_name and author.CollectiveName.string: raw_name = author.CollectiveName.string contrib_extra = dict() orcid = author.find("Identifier", Source="ORCID") if orcid: # needs re-formatting from, eg, "0000000179841889" orcid = orcid.string if orcid.startswith("http://orcid.org/"): orcid = orcid.replace("http://orcid.org/", "") elif orcid.startswith("https://orcid.org/"): orcid = orcid.replace("https://orcid.org/", "") elif not '-' in orcid: orcid = "{}-{}-{}-{}".format( orcid[0:4], orcid[4:8], orcid[8:12], orcid[12:16], ) creator_id = self.lookup_orcid(orcid) contrib_extra['orcid'] = orcid affiliations = author.find_all("Affiliation") raw_affiliation = None if affiliations: raw_affiliation = affiliations[0].string if len(affiliations) > 1: contrib_extra['more_affiliations'] = [ra.string for ra in affiliations[1:]] if author.find("EqualContrib"): # TODO: schema for this? contrib_extra['equal'] = True contribs.append(fatcat_client.ReleaseContrib( raw_name=raw_name, given_name=given_name, surname=surname, role="author", raw_affiliation=raw_affiliation, creator_id=creator_id, extra=contrib_extra, )) if medline.AuthorList['CompleteYN'] == 'N': contribs.append(fatcat_client.ReleaseContrib(raw_name="et al.")) for i, contrib in enumerate(contribs): if contrib.raw_name != "et al.": contrib.index = i if not contribs: contribs = None ### References refs = [] if pubmed.ReferenceList: for ref in pubmed.ReferenceList.find_all('Reference'): ref_extra = dict() ref_pmid = ref.find("ArticleId", IdType="pubmed") ref_doi = ref.find("ArticleId", IdType="doi") ref_release_id = None if ref_pmid: ref_pmid = ref_pmid.string.strip() ref_extra['pmid'] = ref_pmid if self.lookup_refs: ref_release_id = self.lookup_pmid(ref_pmid) if ref_doi: ref_doi = ref_doi.string.lower().strip() ref_extra['doi'] = ref_doi if self.lookup_refs: ref_release_id = self.lookup_doi(ref_doi) ref_raw = ref.Citation if ref_raw: ref_extra['unstructured'] = ref_raw.string if not ref_extra: ref_extra = None refs.append(fatcat_client.ReleaseRef( target_release_id=ref_release_id, extra=ref_extra, )) if not refs: refs = None # extra: # translation_of # subtitle # aliases # container_name # group-title # pubmed: retraction refs if extra_pubmed: extra['pubmed'] = extra_pubmed if not extra: extra = None title = clean(title) if not title: return None re = fatcat_client.ReleaseEntity( work_id=None, title=title, original_title=clean(original_title), release_type=release_type, release_stage=release_stage, release_date=release_date, release_year=release_year, withdrawn_status=withdrawn_status, ext_ids=fatcat_client.ReleaseExtIds( doi=doi, pmid=pmid, pmcid=pmcid, #isbn13 # never in Article ), volume=volume, issue=issue, pages=pages, #publisher # not included? language=language, #license_slug # not in MEDLINE abstracts=abstracts, contribs=contribs, refs=refs, container_id=container_id, extra=extra, ) return re def try_update(self, re): # first, lookup existing by PMID (which must be defined) existing = None try: existing = self.api.lookup_release(pmid=re.ext_ids.pmid) except fatcat_client.rest.ApiException as err: if err.status != 404: raise err # then try DOI lookup if there is one if not existing and re.ext_ids.doi: try: existing = self.api.lookup_release(doi=re.ext_ids.doi) except fatcat_client.rest.ApiException as err: if err.status != 404: raise err if existing and existing.ext_ids.pmid and existing.ext_ids.pmid != re.ext_ids.pmid: warnings.warn("PMID/DOI mismatch: release {}, pmid {} != {}".format( existing.ident, existing.ext_ids.pmid, re.ext_ids.pmid)) self.counts['warn-pmid-doi-mismatch'] += 1 # don't clobber DOI, but do group together re.ext_ids.doi = None re.work_id = existing.work_id if existing and existing.ext_ids.pmid and (existing.refs or not re.refs): # TODO: any other reasons to do an update? # don't update if it already has PMID self.counts['exists'] += 1 return False elif existing: # but do update if only DOI was set existing.ext_ids.doi = existing.ext_ids.doi or re.ext_ids.doi existing.ext_ids.pmid = existing.ext_ids.pmid or re.ext_ids.pmid existing.ext_ids.pmcid = existing.ext_ids.pmcid or re.ext_ids.pmcid existing.refs = existing.refs or re.refs existing.extra['pubmed'] = re.extra['pubmed'] try: self.api.update_release(self.get_editgroup_id(), existing.ident, existing) self.counts['update'] += 1 except fatcat_client.rest.ApiException as err: # there is a code path where we try to update the same release # twice in a row; if that happens, just skip # NOTE: API behavior might change in the future? if "release_edit_editgroup_id_ident_id_key" in err.body: self.counts['skip-update-conflict'] += 1 else: raise err finally: return False return True def insert_batch(self, batch): self.api.create_release_auto_batch(fatcat_client.ReleaseAutoBatch( editgroup=fatcat_client.Editgroup( description=self.editgroup_description, extra=self.editgroup_extra), entity_list=batch)) def parse_file(self, handle): # 1. open with beautiful soup soup = BeautifulSoup(handle, "xml") # 2. iterate over articles, call parse_article on each for article in soup.find_all("PubmedArticle"): resp = self.parse_record(article) print(json.dumps(resp)) #sys.exit(-1) if __name__=='__main__': parser = PubmedImporter(None, None) parser.parse_file(open(sys.argv[1]))