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pmh_record.py
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pmh_record.py
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#!/usr/bin/python
# -*- coding: utf-8 -*-
import datetime
import html
import re
from sqlalchemy import nullslast, or_, orm, text
from sqlalchemy.dialects.postgresql import JSONB
import page
from app import db
from app import logger
from recordthresher.record_maker import PmhRecordMaker
from util import NoDoiException
from util import clean_doi
from util import is_doi_url
from util import normalize_title
DEBUG_BASE = False
_too_common_normalized_titles = None
def too_common_normalized_titles():
global _too_common_normalized_titles
if _too_common_normalized_titles is None:
_too_common_normalized_titles = set([
title for (title, ) in
db.engine.execute(text('select normalized_title from common_normalized_titles'))
])
return _too_common_normalized_titles
def title_is_too_short(normalized_title):
if not normalized_title:
return True
return len(normalized_title) <= 21
def title_is_too_common(normalized_title):
return normalized_title in too_common_normalized_titles()
def is_known_mismatch(doi, pmh_record):
# screen figshare supplemental items, e.g.
# https://doi.org/10.1021/ac035352d vs
# https://api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:figshare.com:article/3339307
if pmh_record.bare_pmh_id and pmh_record.bare_pmh_id.startswith('oai:figshare.com'):
if pmh_record.doi and pmh_record.doi.startswith('{}.s'.format(doi)):
return True
mismatches = {
'10.1063/1.4818552': [
'hdl:10068/886851' # thesis with same title
],
'10.1016/j.conbuildmat.2019.116939': [
'oai:repositorio.cuc.edu.co:11323/5292' # abstract
],
'10.1111/j.1439-0396.2010.01055.x': [
'oai:dspace.uevora.pt:10174/3888' # abstract
],
'10.3233/ves-200717': [
'oai:pure.atira.dk:publications/0eb5fb9c-4e41-4879-970a-78b53b7b078e' # poster with same title
],
'10.1139/p79-106': [
'oai:tsukuba.repo.nii.ac.jp:00011538' # thesis with same title
],
'10.1057/s41296-019-00346-8': [
'oai:eprints.ucl.ac.uk.OAI2:10087912' # wrong pdf on landing page
],
'10.1201/9781315151823': [
'oai:openresearch.lsbu.ac.uk:86zv0' # doi belongs to book, pmh id belongs to chapter
],
'10.1007/s00221-007-1163-1': [
'oai:wrap.warwick.ac.uk:54523' # thesis with same title
],
'10.1080/08989621.2020.1860764': [
'oai:generic.eprints.org:86138' # pdf links don't work, http://irep.iium.edu.my/86138/
],
'10.15866/irease.v11i4.14675': [
'oai:generic.eprints.org:67164' # screenshot of scopus
],
'10.1016/b978-0-12-805393-5.00012-9': [
'oai:CiteSeerX.psu:10.1.1.885.6937' # title parsed incorrectly
],
'10.1007/s10494-020-00126-0': [
'oai:HAL:hal-02195059v1' # conference paper with same title
],
'10.1007/978-1-4614-7163-9_110149-1': [
'oai:HAL:hal-01343052v1' # conference paper with same title
],
'10.1093/epolic/eiaa015': [
# all different papers with same title
'oai::82981',
'oai::92620',
'oai:RePEc:pra:mprapa:82981',
],
'10.1063/1.5114468': [
'oai:www.ucm.es:27329' # conference paper and article with same title
],
'10.1007/978-981-32-9620-6_9': [
'oai:CiteSeerX.psu:10.1.1.434.2367' # citeseerx misfire
],
'10.1093/clinchem/hvaa290': [
'oai:research-information.bris.ac.uk:publications/a61e230c-1d1d-45f6-bdfa-0ed944b93804'
],
}
return pmh_record.bare_pmh_id in mismatches.get(doi, [])
def oai_tag_match(tagname, record, return_list=False):
if not tagname in record.metadata:
return [] if return_list else None
matches = record.metadata[tagname]
if return_list:
return matches # will be empty list if we found naught
else:
try:
return matches[0]
except IndexError: # no matches.
return None
def title_match_limit_exceptions():
return {
'abinitiomoleculardynamicscdsequantumdotdopedglasses',
'speedingupdiscoveryauxeticzeoliteframeworksmachinelearning',
'epigeneticregulationkappaopioidreceptorgeneinsertiondeletionpromoterregion',
}
class PmhRecord(db.Model):
id = db.Column(db.Text, primary_key=True)
repo_id = db.Column(db.Text) # delete once endpoint_ids are all populated
endpoint_id = db.Column(db.Text)
doi = db.Column(db.Text)
record_timestamp = db.Column(db.DateTime)
api_raw = db.Column(JSONB)
title = db.Column(db.Text)
license = db.Column(db.Text)
oa = db.Column(db.Text)
urls = db.Column(JSONB)
authors = db.Column(JSONB)
relations = db.Column(JSONB)
sources = db.Column(JSONB)
updated = db.Column(db.DateTime)
rand = db.Column(db.Numeric)
pmh_id = db.Column(db.Text)
pages = db.relationship(
# 'Page',
'PageNew',
lazy='select', # lazy load
cascade="all, delete-orphan",
# don't want a backref because don't want page to link to this
foreign_keys="PageNew.pmh_id"
)
@property
def bare_pmh_id(self):
return self.pmh_id or self.id
def __init__(self, **kwargs):
self.updated = datetime.datetime.utcnow().isoformat()
super(self.__class__, self).__init__(**kwargs)
def populate(self, endpoint_id, pmh_input_record, metadata_prefix='oai_dc'):
self.updated = datetime.datetime.utcnow().isoformat()
self.id = '{}:{}'.format(endpoint_id, pmh_input_record.header.identifier)
self.endpoint_id = endpoint_id
self.pmh_id = pmh_input_record.header.identifier
self.api_raw = pmh_input_record.raw
self.record_timestamp = pmh_input_record.header.datestamp
self.title = oai_tag_match("title", pmh_input_record)
self.authors = oai_tag_match("creator", pmh_input_record, return_list=True)
self.relations = oai_tag_match("relation", pmh_input_record, return_list=True)
self.oa = oai_tag_match("oa", pmh_input_record)
if metadata_prefix == 'qdc':
self.license = oai_tag_match("rights.license", pmh_input_record)
else:
self.license = oai_tag_match("rights", pmh_input_record)
self.sources = oai_tag_match("collname", pmh_input_record, return_list=True)
identifier_matches = oai_tag_match("identifier", pmh_input_record, return_list=True)
if self.pmh_id and self.pmh_id.startswith('oai:authors.library.caltech.edu'):
identifier_matches = []
if self.pmh_id and self.pmh_id.startswith('oai:deepblue.lib.umich.edu'):
# lots of identifiers and this item's is first
identifier_matches.reverse()
if self.pmh_id and self.pmh_id.startswith('oai:alma.44SUR_INST') or self.pmh_id.startswith('oai:alma.44SUR_INST'):
identifier_matches = oai_tag_match("file.download.url", pmh_input_record, return_list=True)
self.authors = oai_tag_match("creatorname", pmh_input_record, return_list=True)
if self.pmh_id and self.pmh_id.startswith('oai:japanlinkcenter.org'):
identifier_matches = oai_tag_match("url", pmh_input_record, return_list=True)
self.relations = oai_tag_match("related_content", pmh_input_record, return_list=True)
self.authors = []
identifier_doi_matches = oai_tag_match("identifier.doi", pmh_input_record, return_list=True)
identifier_uri_matches = oai_tag_match("identifier.uri", pmh_input_record, return_list=True)
self.urls = self.get_good_urls(identifier_matches + identifier_uri_matches)
if not self.urls:
self.urls = self.get_good_urls(self.relations)
if not self.urls and self.pmh_id and self.pmh_id.startswith('oai:repozytorium.biblos.pk.edu.pl:'):
rpk_id = self.pmh_id.split(':')[-1]
self.urls = [f'https://repozytorium.biblos.pk.edu.pl/resources/{rpk_id}']
possible_dois = []
ignore_relation_prefixes = [
'oai:pantheon.ufrj.br:',
'oai:repository.ucatolica.edu.co:',
'oai:repository.kulib.kyoto-u.ac.jp:',
]
if self.relations and not any(self.bare_pmh_id.startswith(p) for p in ignore_relation_prefixes):
possible_dois += [s for s in self.relations if s and '/*ref*/' not in s and not s.startswith('reference')]
if self.pmh_id and self.pmh_id.startswith('oai:pure.mpg.de:'):
possible_dois.reverse()
if self.bare_pmh_id and self.bare_pmh_id.startswith('oai:openarchive.ki.se:'):
# ticket 22247, relation DOIs are only for this article with this prefix
possible_dois = [s for s in possible_dois if s.startswith('info:eu-repo/semantics/altIdentifier/doi/')]
if identifier_matches:
possible_dois += [s for s in identifier_matches if s]
if identifier_doi_matches:
possible_dois += [s for s in identifier_doi_matches if s]
if self.pmh_id and self.pmh_id.startswith('oai:escholarship.mcgill.ca:'):
possible_dois += oai_tag_match('source', pmh_input_record, return_list=True)
self.set_doi(possible_dois)
self.doi = self._doi_override_by_id().get(self.bare_pmh_id, self.doi)
self.title = self._title_override_by_id().get(self.bare_pmh_id, self.title)
def set_doi(self, possible_dois):
if possible_dois:
for possible_doi in possible_dois:
if (
is_doi_url(possible_doi)
or possible_doi.startswith("doi:")
or re.findall(r"10\.\d", possible_doi)
):
try:
doi_candidate = clean_doi(possible_doi)
if not doi_candidate:
continue
skip_these_doi_snippets = [
'10.17605/osf.io',
'10.14279/depositonce',
'/(issn)',
'10.17169/refubium',
'10.3929/ethz-',
]
skip_these_dois = [
'10.1002/9781118786352', # journal
]
for doi_snippet in skip_these_doi_snippets:
if doi_snippet.lower() in doi_candidate.lower():
doi_candidate = None
break
for skip_doi in skip_these_dois:
if skip_doi and doi_candidate and skip_doi.lower() == doi_candidate.lower():
doi_candidate = None
break
if doi_candidate:
self.doi = doi_candidate
except NoDoiException:
pass
@staticmethod
def _title_override_by_id():
return {
# wrong title
'oai:RePEc:feb:natura:00655': 'Do Workers Value Flexible Jobs? A Field Experiment On Compensating Differentials',
# reviews of books with same title
'oai:ir.uiowa.edu:annals-of-iowa-11115': '(Book Notice) The Bull Moose Years: Theodore Roosevelt and the Progressive Party',
'oai:ir.uiowa.edu:annals-of-iowa-9228': '(Book Review) Land, Piety, Peoplehood: The Establishment of Mennonite Communities in America, 1683-1790',
# published title changed slightly
'oai:figshare.com:article/10272041': 'Ab initio molecular dynamics of CdSe Quantum Dot-Doped Glasses',
# ticket 6010. record links to PDF for different article.
'oai:eprints.uwe.ac.uk:33511': 'The Bristol-Bath Urban freight Consolidation Centre from the perspective of its users',
'oai:www.duo.uio.no:10852/77974': 'Chronic pain among the hospitalized patients after the 22nd july-2011 terror attacks in Oslo and at Utøya Island.',
'oai:lirias2repo.kuleuven.be:123456789/647375': '',
'oai:share.osf.io:460F8-921-B0C': 'How optimal is word recognition under multimodal uncertainty?',
'oai:zenodo.org:5772413': 'Compensation Strategies for Gait Impairments in Parkinson Disease',
}
@staticmethod
def _doi_override_by_id():
return {
# wrong DOI in identifier url
'oai:dspace.flinders.edu.au:2328/36108': '10.1002/eat.22455',
# picked up wrong DOI in relation
'oai:oai.kemsu.elpub.ru:article/2590': '10.21603/2078-8975-2018-4-223-231',
# junk in identifier
'oai:scholarspace.manoa.hawaii.edu:10125/42031': '10.18357/ijih122201717783',
# wrong DOI in relation
'oai:oai.perinatology.elpub.ru:article/560': '10.21508/1027-4065-2017-62-5-111-118',
'oai:HAL:hal-00927061v2': '10.1090/memo/1247',
'oai:revistas.ucm.es:article/62495': '10.5209/clac.62495',
'oai:oro.open.ac.uk:57403': '10.1090/hmath/011',
'oai:eprints.soas.ac.uk:22576': '10.4324/9781315762210-8',
'oai:oai.mir.elpub.ru:article/838': '10.18184/2079-4665.2018.9.3.338-350',
'oai:arXiv.org:1605.06120': None,
'oai:research-repository.griffith.edu.au:10072/80920': None,
'oai:HAL:cea-01550620v1': '10.1103/physrevb.93.214414',
'oai:ora.ox.ac.uk:uuid:f5740dd3-0b45-4e7b-8f2e-d4872a6c326c': '10.1016/j.jclinepi.2017.12.022',
'oai:ora.ox.ac.uk:uuid:a78ee943-6cfe-4fb9-859e-d7ec82ebec85': '10.1016/j.jclinepi.2019.05.033',
'oai:archive.ugent.be:3125191': None,
'oai:scholar.sun.ac.za:10019.1/95408': '10.4102/sajpsychiatry.v19i3.951',
'oai:rcin.org.pl:60213': None,
'oai:rcin.org.pl:48382': None,
'oai:philarchive.org/rec/LOGSTC': '10.1093/analys/anw051',
'oai:philarchive.org/rec/LOGMBK': '10.1111/1746-8361.12258',
'oai:CiteSeerX.psu:10.1.1.392.2251': None,
'oai:serval.unil.ch:BIB_289289AA7E27': None, # oai:serval.unil.ch:duplicate of BIB_98991EE549F6
'oai:deepblue.lib.umich.edu:2027.42/141967': '10.1111/asap.12132',
'oai:eprints.lancs.ac.uk:80508': None, # says 10.1057/978-1-137-58629-2, but that's the book holding this chapter
'oai:zenodo.org:3994623': '10.1007/978-3-319-29791-0',
'oai:elib.dlr.de:136158': None, # chapter of 10.1007/978-3-030-48340-1
'oai:wrap.warwick.ac.uk:147355': '10.1177/0022242921992052',
'oai:www.zora.uzh.ch:133251': None,
'oai:ray.yorksj.ac.uk:2511': None, # record is chapter, DOI is book
'oai:intellectum.unisabana.edu.co:10818/20216': None, # all DOIs are citations
'oai:cris.maastrichtuniversity.nl:publications/494aa88b-4a2b-4b81-b926-8005af3f85d5': None, # record is chapter, DOI is book
'oai:repository.ucatolica.edu.co:10983/22919': '10.14718/revarq.2018.20.2.1562',
'oai:HAL:halshs-03107637v1': None, # record is chapter, DOI 10.1515/9781614514909 is book
'oai:eprints.bbk.ac.uk.oai2:28966': '10.1007/978-3-030-29736-7_11', # book chapter
'oai:dspace.library.uvic.ca:1828/11889': None,
'oai:real.mtak.hu:122999': None,
'oai:real.mtak.hu:121388': None,
'oai:arXiv.org:1306.1461': None,
'oai:lirias2repo.kuleuven.be:123456789/647375': None,
'oai:strathprints.strath.ac.uk:65258': None, # record is chapter, DOI is book
'oai:research-repository.griffith.edu.au:10072/389013': None, # only a summary
'oai:e-space.mmu.ac.uk:618539': None, # bad DOI fom relation
'oai:alma61RMIT.INST:11247217330001341': None, # book/chapter
'oai:repository.unab.edu.co:20.500.12749/2107': None,
'oai:HAL:hal-03157274v1': '10.1080/00220388.2020.1715942',
'oai:zenodo.org:2414272': None,
# book chapters
'oai:trepo.tuni.fi:10024/118421': None,
'oai:www.duo.uio.no:10852/76264': None,
'oai:www.duo.uio.no:10852/76567': None,
'oai:research-repository.griffith.edu.au:10072/380027': None,
'oai:eprints.leedsbeckett.ac.uk:5899': None,
'oai:openresearch.lsbu.ac.uk:8yyz8': None,
'oai:openaccess.city.ac.uk:15995': '10.1016/j.insmatheco.2012.12.009',
# book chapter
'oai:air.unimi.it:2434/707996': None,
'oai:iris.unive.it:10278/3734529': '10.1007/978-3-319-20791-9_314-1',
'oai:repozytorium.amu.edu.pl:10593/6693': None,
'b2002691-9888-4c9e-900a-91bdad900d8b/oai:repozytorium.amu.edu.pl:10593/6693': None,
'oai:boa.unimib.it:10281/3095': None,
'oai:eprints.nottingham.ac.uk:42938': None,
'oai:nottingham-repository.worktribe.com:744398': None,
'oai:centaur.reading.ac.uk:37024': None,
'oai:sure.sunderland.ac.uk:9399': None,
'oai:sure.sunderland.ac.uk:9330': None,
'oai:sure.sunderland.ac.uk:10188': None,
'oai:sure.sunderland.ac.uk:10190': None,
'oai:sure.sunderland.ac.uk:9176': None,
'oai:sure.sunderland.ac.uk:10630': None,
'oai:sure.sunderland.ac.uk:9304': None,
'oai:sure.sunderland.ac.uk:9175': None,
'oai:sure.sunderland.ac.uk:9873': None,
'oai:sure.sunderland.ac.uk:9930': None,
'oai:sure.sunderland.ac.uk:9755': None,
'oai:arXiv.org:hep-ph/0404005': None,
'oai:arXiv.org:1212.3347': '10.4169/math.mag.86.2.143',
'oai:westminsterresearch.westminster.ac.uk:929yw' : None,
'oai:research-information.bris.ac.uk:publications/a61e230c-1d1d-45f6-bdfa-0ed944b93804': None,
'oai:tara.tcd.ie:2262/91798': '10.1017/ipm.2017.80',
'oai:gupea.ub.gu.se:2077/66303': None,
'oai:repository.ucatolica.edu.co:10983/26325': None,
}
def get_good_urls(self, candidate_urls):
valid_urls = []
# pmc can only add pmc urls. otherwise has junk about dois that aren't actually open.
if candidate_urls:
if "oai:pubmedcentral.nih.gov" in self.id:
for url in candidate_urls:
if "/pmc/" in url and url != "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC":
pmcid_matches = re.findall(".*(PMC\d+).*", url)
if pmcid_matches:
pmcid = pmcid_matches[0]
url = "https://www.ncbi.nlm.nih.gov/pmc/articles/{}".format(pmcid)
valid_urls.append(url)
else:
if self.endpoint_id == 'ycf3gzxeiyuw3jqwjmx3': # https://lirias.kuleuven.be
candidate_urls = [re.sub(r'^\d+;http', 'http', url) for url in candidate_urls if url]
valid_urls += [url for url in candidate_urls if url and url.startswith("http")]
if self.pmh_id and self.pmh_id.startswith('oai:RePEc:'):
repec_handle = re.sub(r'^oai:', '', self.pmh_id)
return [f'https://econpapers.repec.org/{repec_handle}']
# filter out doi urls unless they are the only url
# might be a figshare url etc, but otherwise is usually to a publisher page which
# may or may not be open, and we are handling through hybrid path
use_doi_url_id_prefixes = [
'cdr.lib.unc.edu:',
]
use_doi_url = False
for use_doi_url_id_prefix in use_doi_url_id_prefixes:
if self.bare_pmh_id and self.bare_pmh_id.startswith(use_doi_url_id_prefix):
use_doi_url = True
break
if not use_doi_url and len(valid_urls) > 1:
valid_urls = [url for url in valid_urls if "doi.org/" not in url]
valid_urls = [url for url in valid_urls if "doi.org/10.1111/" not in url]
if self.bare_pmh_id and self.bare_pmh_id.startswith('oai:alma.61RMIT_INST:'):
valid_urls = [url for url in valid_urls if 'rmit.edu.au' in url]
if self.bare_pmh_id and self.bare_pmh_id.startswith('oai:pure.rug.nl:'):
valid_urls = [url for url in valid_urls if 'rug.nl' in url]
# filter out some urls that we know are closed or otherwise not useful
blacklist_url_snippets = [
"/10.1093/analys/",
"academic.oup.com/analysis",
"analysis.oxfordjournals.org/",
"ncbi.nlm.nih.gov/pubmed/",
"gateway.webofknowledge.com/",
"orcid.org/",
"researchgate.net/",
"academia.edu/",
"europepmc.org/abstract/",
"ftp://",
"api.crossref",
"api.elsevier",
"api.osf",
"eprints.soton.ac.uk/413275",
"eprints.qut.edu.au/91459/3/91460.pdf",
"hdl.handle.net/2117/168732",
"hdl.handle.net/10044/1/81238", # wrong article
"journals.elsevier.com",
"https://hdl.handle.net/10037/19572", # copyright violation. ticket 22259
"http://irep.iium.edu.my/58547/9/Antibiotic%20dosing%20during%20extracorporeal%20membrane%20oxygenation.pdf",
"oceanrep.geomar.de/52096/7/s41586-021-03496-1.pdf",
"eprints.lmu.edu.ng/3516/",
"springerlink.com/content/",
]
backlist_url_patterns = list(map(re.escape, blacklist_url_snippets)) + [
r'springer.com/.*/journal/\d+$',
r'springer.com/journal/\d+$',
r'supinfo\.pdf$',
r'\dfigures\.pdf$',
r'\dsupplemental\.pdf$',
r'Appendix[^/]*\.pdf$',
r'^https?://www\.icgip\.org/?$',
r'^https?://(www\.)?agu.org/journals/',
r'issue/current$',
r'/809AB601-EF05-4DD1-9741-E33D7847F8E5\.pdf$',
r'onlinelibrary\.wiley\.com/doi/',
r'https?://doi\.org/10\.1002/', # wiley
r'https?://doi\.org/10\.1111/', # wiley
r'https?://doi\.org/10\.1007/', # springer
r'authors\.library\.caltech\.edu/93971/\d+/41562_2019_595_MOESM',
r'aeaweb\.org/.*\.ds$',
r'aeaweb\.org/.*\.data$',
r'aeaweb\.org/.*\.appx$',
r'https?://dspace\.stir\.ac\.uk/.*\.jpg$',
r'https?://dspace\.stir\.ac\.uk/.*\.tif$',
r'/table_final\.pdf$',
r'/supplemental_final\.pdf$',
r'psasir\.upm\.edu\.my/id/eprint/36880/1/Conceptualizing%20and%20measuring%20youth\.pdf',
r'psasir\.upm\.edu\.my/id/eprint/53326/1/Conceptualizing%20and%20measuring%20youth\.pdf',
r'^https?://(www\.)?tandfonline\.com/toc/',
r'\dSuppl\.pdf$',
r'^https://lirias\.kuleuven\.be/handle/\d+/\d+$',
r'^https?://eu\.wiley\.com/',
r'^https?://www\.wiley\.com/',
r'hull-repository\.worktribe\.com/(\w+/)?437540(/|$)',
r'researchonline\.jcu\.edu\.au/.*_cover.pdf',
]
for url_snippet in backlist_url_patterns:
valid_urls = [url for url in valid_urls if not re.search(url_snippet, url)]
supplemental_url_patterns = [
r'Figures.pdf$',
]
if len(valid_urls) > 1:
for url_pattern in supplemental_url_patterns:
valid_urls = [url for url in valid_urls if not re.search(url_pattern, url)]
# and then html unescape them, because some are html escaped
valid_urls = [html.unescape(url) for url in valid_urls]
# make sure they are actually urls
valid_urls = [url for url in valid_urls if url.startswith("http")]
if self.bare_pmh_id.startswith('oai:ora.ox.ac.uk:uuid:') and not valid_urls:
# https://ora.ox.ac.uk
# pmh records don't have page urls but we can guess them
# remove 'oai:ora.ox.ac.uk:' prefix and append to base URL
valid_urls.append('https://ora.ox.ac.uk/objects/{}'.format(self.bare_pmh_id[len('oai:ora.ox.ac.uk:'):]))
valid_urls = list(set(valid_urls))
return valid_urls
def mint_repo_page_for_url(self, url):
my_repo_page = self.mint_page_for_url(page.RepoPage, url)
# get the most recent scrape data
most_recent_old_page = page.PageNew.query.filter(
page.PageNew.endpoint_id == self.endpoint_id,
page.PageNew.url == url
).order_by(
nullslast(page.PageNew.scrape_updated.desc())
).options(orm.noload('*')).first()
if most_recent_old_page:
my_repo_page.scrape_updated = most_recent_old_page.scrape_updated
my_repo_page.scrape_metadata_url = most_recent_old_page.scrape_metadata_url
my_repo_page.scrape_pdf_url = most_recent_old_page.scrape_pdf_url
my_repo_page.scrape_license = most_recent_old_page.scrape_license
my_repo_page.scrape_version = most_recent_old_page.scrape_version
return my_repo_page
def mint_page_for_url(self, page_class, url):
from page import PageNew
# this is slow, but no slower than looking for titles before adding pages
existing_page = PageNew.query.filter(PageNew.normalized_title==self.calc_normalized_title(),
PageNew.match_type==page_class.__mapper_args__["polymorphic_identity"],
PageNew.url==url,
PageNew.endpoint_id==self.endpoint_id
).options(orm.noload('*')).first()
if existing_page:
my_page = existing_page
else:
my_page = page_class()
my_page.url = url
my_page.normalized_title = self.calc_normalized_title()
my_page.endpoint_id = self.endpoint_id
my_page.doi = self.doi
my_page.title = self.title
my_page.authors = self.authors
my_page.record_timestamp = self.record_timestamp
my_page.pmh_id = self.id
my_page.repo_id = self.repo_id # delete once endpoint_ids are all populated
my_page.pmh_record = self
return my_page
def calc_normalized_title(self):
if not self.title:
return None
if self.endpoint_id == '63d70f0f03831f36129':
# figshare. the record is for a figure but the title is from its parent article.
if not self.doi and re.match(r'10\.36227/techrxiv\.\d+(?:\.v\n+)?', self.doi):
return None
working_title = self.title
# repo specific rules
# AMNH adds biblio to the end of titles, which ruins match. remove this.
# example http://digitallibrary.amnh.org/handle/2246/6816 oai:digitallibrary.amnh.org:2246/6816
if "amnh.org" in self.id:
# cut off the last part, after an openning paren
working_title = re.sub("(Bulletin of.+no.+\d+)", "", working_title, re.IGNORECASE | re.MULTILINE)
working_title = re.sub("(American Museum nov.+no.+\d+)", "", working_title, re.IGNORECASE | re.MULTILINE)
# for endpoint 0dde28a908329849966, adds this to end of all titles, so remove (eg http://hdl.handle.net/11858/00-203Z-0000-002E-72BD-3)
working_title = re.sub("vollständige digitalisierte Ausgabe", "", working_title, re.IGNORECASE | re.MULTILINE)
return normalize_title(working_title)
def delete_old_record(self):
# old records used the bare record_id as pmh_record.id
# delete the old record before merging, instead of conditionally updating or creating the new record
db.session.query(PmhRecord).filter(
PmhRecord.id == self.bare_pmh_id, PmhRecord.endpoint_id == self.endpoint_id
).delete()
def mint_pages(self, reset_scrape_date=False):
if self.endpoint_id == 'ac9de7698155b820de7':
# NIH PMC. Don't mint pages because we use a CSV dump to make OA locations. See Pub.ask_pmc
return []
if self.bare_pmh_id and self.bare_pmh_id.startswith('oai:openarchive.ki.se:'):
# ticket 22247, only type=art can match DOIs
if '<dc:type>art</dc:type>' not in self.api_raw:
return []
self.pages = []
# this should have already been done when setting .urls, but do it again in case there were improvements
# case in point: new url patterns added to the blacklist
good_urls = self.get_good_urls(self.urls)
if re.compile(r'<dc:rights>Limited Access</dc:rights>', re.MULTILINE).findall(self.api_raw):
logger.info('found limited access label, not minting pages')
else:
for url in good_urls:
my_repo_page = self.mint_repo_page_for_url(url)
if self.doi:
my_repo_page.match_doi = True
normalized_title = self.calc_normalized_title()
if normalized_title:
num_pages_with_this_normalized_title = db.session.query(page.RepoPage.id).filter(
page.RepoPage.match_title == True,
page.RepoPage.normalized_title == normalized_title
).count()
if (
num_pages_with_this_normalized_title >= 20
and normalized_title not in title_match_limit_exceptions()
and "oai:HAL:" not in self.bare_pmh_id
):
logger.info(
"not allowing title matches because too many with this title: {}".format(
normalized_title
)
)
elif self.bare_pmh_id and self.bare_pmh_id.startswith("oai:mdpi.com:"):
# publisher site, don't match to other DOIs by title
pass
else:
my_repo_page.match_title = True
self.pages.append(my_repo_page)
# logger.info(u"minted pages: {}".format(self.pages))
# delete pages with this pmh_id that aren't being updated
db.session.query(page.PageNew).filter(
page.PageNew.endpoint_id == self.endpoint_id,
or_(page.PageNew.pmh_id == self.id, page.PageNew.pmh_id == self.pmh_id),
page.PageNew.id.notin_([p.id for p in self.pages])
).delete(synchronize_session=False)
if reset_scrape_date and self.pages:
# move already queued-pages at the front of the queue
# if the record was updated the oa status might have changed
query_text = '''
update page_green_scrape_queue
set finished = null
where id = any(:ids) and started is null
'''
reset_query = text(query_text).bindparams(ids=[p.id for p in self.pages])
db.session.execute(reset_query)
return self.pages
def enqueue_representative_page(self):
# if recordthresher is going to try to make a record based on a page, enqueue it now
if rp := PmhRecordMaker.representative_page(self):
db.session.merge(page.PageGreenScrapeQueue(id=rp.id, endpoint_id=rp.endpoint_id))
def __repr__(self):
return "<PmhRecord ({}) doi:{} '{}...'>".format(self.id, self.doi, self.title[0:20])
def to_dict(self):
response = {
"oaipmh_id": self.bare_pmh_id,
"oaipmh_record_timestamp": self.record_timestamp and self.record_timestamp.isoformat(),
"urls": self.urls,
"title": self.title
}
return response