Coverage for src / crawler / abstract_crawlers / base_crawler.py: 65%

1import logging 

2import time 

3from collections.abc import Iterable 

4from datetime import datetime, timedelta 

5from email.policy import EmailPolicy 

6from typing import TYPE_CHECKING, Literal 

7 

8import aiohttp 

9import regex 

10import requests 

11from bs4 import BeautifulSoup 

12from django.conf import settings 

13from django.contrib.auth.models import User 

14from django.db.utils import IntegrityError 

15from django.utils import timezone 

16from langcodes import standardize_tag 

17from lingua import LanguageDetector, LanguageDetectorBuilder 

18from opentelemetry import trace 

19from ptf.cmds.xml.ckeditor.utils import ( 

20 build_jats_data_from_html_field, 

21) 

22from ptf.cmds.xml.jats.builder.references import ( 

23 get_article_title_xml, 

24 get_author_xml, 

25 get_fpage_xml, 

26 get_lpage_xml, 

27 get_source_xml, 

28 get_year_xml, 

29) 

30from ptf.cmds.xml.jats.jats_parser import JatsBase 

31from ptf.model_data import ( 

32 ArticleData, 

33 ContributorDict, 

34 IssueData, 

35 ResourceData, 

36 TitleDict, 

37 create_abstract, 

38 create_contributor, 

39 create_extlink, 

40 create_issuedata, 

41 create_publisherdata, 

42 create_subj, 

43 create_titledata, 

44) 

45from ptf.model_data_converter import update_data_for_jats 

46from ptf.models import ExtLink 

47from pylatexenc.latex2text import LatexNodes2Text 

48from pysolr import SolrError 

49from requests.adapters import HTTPAdapter 

50from requests_cache import CachedSession 

51from urllib3 import Retry 

52 

53from crawler.cmds.xml_cmds import addOrUpdateGDMLIssueXmlCmd 

54from crawler.models import Source 

55from crawler.models.extlink_checked import ExtlinkChecked 

56from crawler.types import CitationLiteral 

57from crawler.utils import ( 

58 add_pdf_link_to_xarticle, 

59 cleanup_str, 

60 get_all_cols, 

61 get_or_create_collection, 

62 get_session, 

63) 

64 

65if TYPE_CHECKING: 

66 from bs4 import Tag 

67 

68 

69class CrawlerTitleDict(TitleDict): 

70 title_tex: str | None 

71 

72 

73class BaseCollectionCrawler: 

74 """ 

75 Base collection for the crawlers. 

76 To create a crawler: 

77 1) derive a class from BaseCollectionCrawler and name it XXXCrawler 

78 2) override the functions parse_collection_content, parse_issue_content and parse_article_content 

79 3) update factory.py so that crawler_factory can return your new crawler 

80 """ 

81 

82 logger = logging.getLogger(__name__) 

83 tracer = trace.get_tracer(__name__) 

84 

85 source_name = "" 

86 source_domain = "" 

87 source_website = "" 

88 

89 issue_href = "" 

90 

91 collection = None 

92 source = None 

93 user = None 

94 session: requests.Session | CachedSession 

95 async_session: aiohttp.ClientSession 

96 is_checkable = True 

97 verify = True 

98 headers = { 

99 "accept_encoding": "utf-8", 

100 "User-Agent": getattr(settings, "REQUESTS_USER_AGENT", "Mathdoc/1.0.0"), 

101 "From": getattr(settings, "REQUESTS_EMAIL", "accueil@listes.mathdoc.fr"), 

102 } 

103 

104 # seconds to wait between two http requests 

105 requests_interval = getattr(settings, "REQUESTS_INTERVAL", 90) 

106 # seconds to wait before aborting the connection (if no bytes are recieved) 

107 requests_timeout = 60 

108 

109 latext_parser = LatexNodes2Text() 

110 

111 # Override the values in your concrete crawler if the formulas in text (titles, abstracts) 

112 # do not use the "$" to surround tex formulas 

113 delimiter_inline_formula = "$" 

114 delimiter_disp_formula = "$" 

115 

116 # HACK : Workaround for tests (monkeypatching) 

117 # We store the class here, so we can monkeypatch it when running tests 

118 # subCrawlers = { 

119 # LofplCrawler: None 

120 # } 

121 subCrawlers: dict[type["BaseCollectionCrawler"], "BaseCollectionCrawler | None"] = {} 

122 

123 _language_detector: LanguageDetector | None = None 

124 _language_detector_builder = LanguageDetectorBuilder.from_all_languages() 

125 

126 force_refresh = False 

127 

128 # Whereas to include headers in requests cache key 

129 match_headers = False 

130 orcid_re = r"https\:\/\/orcid\.org\/(?P<orcid>\d{4}-\d{4}-\d{4}-\d{4})" 

131 

132 # Set this to False on a Crawler-basis to allow inserting articles without PDFs 

133 ignore_missing_pdf = True 

134 

135 @classmethod 

136 def get_view_id(cls): 

137 return cls.source_domain 

138 

139 @property 

140 def language_detector(self): 

141 """Crawler Instance singleton for language builder. 

142 Late init of LanguageDetector to save on memory""" 

143 if not self._language_detector: 

144 self._language_detector = self._language_detector_builder.build() 

145 return self._language_detector 

146 

147 def __init__( 

148 self, 

149 *args, 

150 username: str, 

151 collection_id: str, 

152 dry: bool = False, 

153 publisher: str = "", 

154 force_refresh=False, 

155 collection_url: str | None = None, 

156 ): 

157 if not collection_url: 157 ↛ 158line 157 didn't jump to line 158 because the condition on line 157 was never true

158 all_cols = get_all_cols() 

159 col = all_cols[collection_id] 

160 

161 collection_url = col["sources"].get(self.source_domain, None) 

162 if collection_url is None: 

163 raise ValueError( 

164 f"Source {self.source_domain} not found for collection {collection_id}" 

165 ) 

166 self.collection_url = collection_url 

167 for CrawlerClass in self.subCrawlers: 167 ↛ 168line 167 didn't jump to line 168 because the loop on line 167 never started

168 self.subCrawlers[CrawlerClass] = CrawlerClass( 

169 *args, 

170 username=username, 

171 collection_id=collection_id, 

172 dry=dry, 

173 publisher=publisher, 

174 collection_url=collection_url, 

175 ) 

176 self.logger = logging.getLogger(__name__ + "." + self.source_domain) 

177 # self.logger = logging.getLogger(__name__) 

178 

179 self.username = username 

180 

181 self.collection_id = collection_id 

182 

183 self.dry = dry 

184 self.publisher = publisher 

185 

186 # Classproperty : We sometimes want to use the session without initializing the class (rot monitoring) 

187 BaseCollectionCrawler.session = requests.Session() 

188 

189 # Skipped when running tests 

190 self.initialize() 

191 

192 self.force_refresh = force_refresh 

193 

194 # We implemented custom retry behaviour, so we don't want to make extra requests here 

195 

196 def initialize(self): 

197 """ 

198 Acts as a "second" init function to skip model accesses during test data generation 

199 """ 

200 self.collection = get_or_create_collection(self.collection_id) 

201 self.source = self.get_or_create_source() 

202 self.user = User.objects.get(username=self.username) 

203 BaseCollectionCrawler.session = get_session() 

204 BaseCollectionCrawler.session.verify = self.verify 

205 self.session.delay = self.requests_interval 

206 retries = Retry( 

207 total=0, 

208 ) 

209 self.session.mount("https://", HTTPAdapter(max_retries=retries)) 

210 self.session.mount("http://", HTTPAdapter(max_retries=retries)) 

211 

212 @classmethod 

213 def can_crawl(cls, pid: str) -> bool: 

214 return True 

215 

216 def parse_collection_content(self, content: str) -> list[IssueData]: 

217 """ 

218 Parse the HTML content with BeautifulSoup 

219 returns a list of xissue. 

220 Override this function in a derived class 

221 """ 

222 return [] 

223 

224 def parse_issue_content(self, content: str, xissue: IssueData): 

225 """ 

226 Parse the HTML content with BeautifulSoup 

227 Fills the xissue.articles 

228 Override this function in a derived class. 

229 

230 CAV : You are supposed to create articles there. Please assign a PID to each article. 

231 The PID can be `a + article_index`, like this : `a0` `a21` 

232 """ 

233 

234 def parse_article_content( 

235 self, content: str, xissue: IssueData, xarticle: ArticleData, url: str 

236 ) -> ArticleData | None: 

237 """ 

238 Parse the HTML content with BeautifulSoup 

239 returns the xarticle. 

240 Override this function in a derived class. 

241 The xissue is passed to the function in case the article page has issue information (ex: publisher) 

242 The article url is also passed as a parameter 

243 

244 CAV : You are supposed to assign articles pid again here 

245 """ 

246 return xarticle 

247 

248 @tracer.start_as_current_span("crawl_collection") 

249 def crawl_collection(self): 

250 # TODO: Comments, filter 

251 """ 

252 Crawl an entire collection. ptf.models.Container objects are created. 

253 - get the HTML content of the collection_url 

254 - parse the HTML content with beautifulsoup to extract the list of issues 

255 - merge the xissues (some Source can have multiple pages for 1 volume/issue. We create only 1 container) 

256 - crawl each issue if col_only is False 

257 - Returns the list of merged issues. 

258 It is an OrderedDict {pid: {"issues": xissues}} 

259 The key is the pid of the merged issues. 

260 Ex: The source may have Ex: Volume 6 (2000) and Volume 6 (1999) 

261 the pid is then made with 1999-2000__6_ 

262 """ 

263 

264 if self.source is None: 

265 raise RuntimeError("ERROR: the source is not set") 

266 

267 content = self.download_file(self.collection_url) 

268 if content: 

269 xissues = self.parse_collection_content(content) 

270 else: 

271 # download_file returns None (404) 

272 return None 

273 

274 """ 

275 Some collections split the same volumes in different pages 

276 Ex: Volume 6 (2000) and Volume 6 (1999) 

277 We merge the 2 xissues with the same volume number => Volume 6 (1999-2000) 

278 """ 

279 # merged_xissues = self.merge_xissues(xissues) 

280 

281 xissues_dict = {str(i.pid): i for i in xissues} 

282 

283 return xissues_dict 

284 

285 @tracer.start_as_current_span("crawl_issue") 

286 def crawl_issue(self, xissue: IssueData): 

287 """ 

288 Crawl 1 wag page of an issue. 

289 - get the HTML content of the issue 

290 - parse the HTML content with beautifulsoup to extract the list of articles and/or the issue metadata 

291 - crawl each article 

292 """ 

293 # Some source, like EuDML do not have a separate HTML pages for an issue's table of content. 

294 # The list of articles directly come from the collection HTML page: the xissue has no url attribute 

295 issue_url = xissue.url 

296 if issue_url is not None: 

297 if issue_url.endswith(".pdf"): 

298 add_pdf_link_to_xarticle(xissue, issue_url) 

299 xissue.url = None 

300 else: 

301 content = self.download_file(issue_url) 

302 with self.tracer.start_as_current_span("parse_issue_content"): 

303 self.parse_issue_content(content, xissue) 

304 

305 xarticles = xissue.articles 

306 

307 parsed_xarticles = [] 

308 

309 for xarticle in xarticles: 

310 parsed_xarticle = self.crawl_article(xarticle, xissue) 

311 if parsed_xarticle is not None: 

312 parsed_xarticles.append(parsed_xarticle) 

313 

314 xissue.articles = parsed_xarticles 

315 

316 issue_has_pdf = self.article_has_pdf(xissue) 

317 

318 if self.ignore_missing_pdf: 

319 xissue.articles = [a for a in xissue.articles if self.article_has_pdf(a)] 

320 if self.dry: 

321 return 

322 if len(xissue.articles) == 0 and not issue_has_pdf: 

323 return 

324 self.process_resource_metadata(xissue, resource_type="issue") 

325 

326 self.add_xissue_into_database(xissue) 

327 

328 @staticmethod 

329 def article_has_source(art: ArticleData | IssueData): 

330 return ( 

331 next( 

332 (e_link for e_link in art.ext_links if e_link["rel"] == "source"), 

333 None, 

334 ) 

335 is not None 

336 ) 

337 

338 @staticmethod 

339 def article_has_pdf(art: ArticleData | IssueData): 

340 return ( 

341 next( 

342 (link for link in art.ext_links if link["rel"] in ["article-pdf", "article-html"]), 

343 None, 

344 ) 

345 is not None 

346 ) 

347 

348 def crawl_article(self, xarticle: ArticleData, xissue: IssueData): 

349 # ARTICLE URL as en ExtLink (to display the link in the article page) 

350 if xarticle.url is None: 

351 if not self.article_has_source(xarticle): 351 ↛ 361line 351 didn't jump to line 361 because the condition on line 351 was always true

352 if xissue.url: 

353 article_source = xissue.url 

354 else: 

355 article_source = self.collection_url 

356 ext_link = create_extlink() 

357 ext_link["rel"] = "source" 

358 ext_link["location"] = article_source 

359 ext_link["metadata"] = self.source_domain 

360 xarticle.ext_links.append(ext_link) 

361 return self.process_article_metadata(xarticle) 

362 

363 content = self.download_file(xarticle.url) 

364 xarticle.pid = f"{xissue.pid}_{xarticle.pid}" 

365 

366 try: 

367 with self.tracer.start_as_current_span("parse_article_content"): 

368 parsed_xarticle = self.parse_article_content( 

369 content, xissue, xarticle, xarticle.url 

370 ) 

371 except ValueError as e: 

372 self.logger.warning(e) 

373 self.logger.warning("Retrying in 5 mins while invalidating cache") 

374 time.sleep(5 * 60) 

375 content = self.download_file(xarticle.url, force_refresh=True) 

376 with self.tracer.start_as_current_span("parse_article_content"): 

377 parsed_xarticle = self.parse_article_content( 

378 content, xissue, xarticle, xarticle.url 

379 ) 

380 

381 if parsed_xarticle is None: 381 ↛ 382line 381 didn't jump to line 382 because the condition on line 381 was never true

382 return None 

383 

384 if parsed_xarticle.doi: 

385 parsed_xarticle.pid = ( 

386 parsed_xarticle.doi.replace("/", "_").replace(".", "_").replace("-", "_") 

387 ) 

388 

389 if not self.article_has_source(parsed_xarticle) and parsed_xarticle.url: 

390 ext_link = create_extlink() 

391 ext_link["rel"] = "source" 

392 ext_link["location"] = parsed_xarticle.url 

393 ext_link["metadata"] = self.source_domain 

394 parsed_xarticle.ext_links.append(ext_link) 

395 

396 # The article title may have formulas surrounded with '$' 

397 return self.process_article_metadata(parsed_xarticle) 

398 

399 def process_resource_metadata(self, xresource: ResourceData, resource_type="article"): 

400 tag = "article-title" if resource_type == "article" else "issue-title" 

401 

402 # Process title tex 

403 ckeditor_data = build_jats_data_from_html_field( 

404 xresource.title_tex, 

405 tag=tag, 

406 text_lang=xresource.lang, 

407 delimiter_inline=self.delimiter_inline_formula, 

408 delimiter_disp=self.delimiter_disp_formula, 

409 ) 

410 

411 xresource.title_html = ckeditor_data["value_html"] 

412 # xresource.title_tex = ckeditor_data["value_tex"] 

413 xresource.title_xml = ckeditor_data["value_xml"] 

414 

415 # Process trans_title tex 

416 if xresource.trans_title_tex: 416 ↛ 417line 416 didn't jump to line 417 because the condition on line 416 was never true

417 self.logger.warning( 

418 "Deprecation Notice : prefer using xresource.title directly instead of xresource.trans_title_tex" 

419 ) 

420 trans_title = self.create_trans_title( 

421 xresource_lang=xresource.lang, 

422 resource_type=resource_type, 

423 title_tex=xresource.trans_title_tex, 

424 lang=xresource.trans_lang, 

425 ) 

426 xresource.titles.append(trans_title) 

427 

428 abstracts_to_parse = [ 

429 xabstract for xabstract in xresource.abstracts if xabstract["tag"] == "abstract" 

430 ] 

431 # abstract may have formulas surrounded with '$' 

432 if len(abstracts_to_parse) > 0: 

433 for xabstract in abstracts_to_parse: 

434 ckeditor_data = build_jats_data_from_html_field( 

435 xabstract["value_tex"], 

436 tag="abstract", 

437 text_lang=xabstract["lang"], 

438 resource_lang=xresource.lang, 

439 field_type="abstract", 

440 delimiter_inline=self.delimiter_inline_formula, 

441 delimiter_disp=self.delimiter_disp_formula, 

442 ) 

443 

444 xabstract["value_html"] = ckeditor_data["value_html"] 

445 # xabstract["value_tex"] = ckeditor_data["value_tex"] 

446 xabstract["value_xml"] = ckeditor_data["value_xml"] 

447 

448 return xresource 

449 

450 def process_article_metadata(self, xarticle: ArticleData): 

451 self.process_resource_metadata(xarticle) 

452 for bibitem in xarticle.bibitems: 

453 bibitem.type = "unknown" 

454 update_data_for_jats(xarticle, with_label=False) 

455 

456 return xarticle 

457 

458 def download_file(self, url: str, force_refresh=False, headers={}): 

459 """ 

460 Downloads a page and returns its content (decoded string). 

461 This function handles retries and decoding 

462 """ 

463 current_exception: Exception | None = None 

464 for attempt in range(3): 

465 try: 

466 kwargs = { 

467 "url": url, 

468 "headers": {**self.headers, **headers}, 

469 "timeout": self.requests_timeout, 

470 } 

471 if attempt > 0 and isinstance(self.session, CachedSession): 

472 kwargs["force_refresh"] = True 

473 response = self.session.get(**kwargs) 

474 

475 content = self.decode_response(response) 

476 if content == "" or not content: 

477 raise requests.exceptions.HTTPError(response) 

478 

479 return content 

480 except ( 

481 requests.ConnectionError, 

482 requests.ConnectTimeout, 

483 requests.exceptions.HTTPError, 

484 ) as e: 

485 current_exception = e 

486 self.logger.debug(f"Caught error : {e}", extra={"url": url}) 

487 # 15 mins, 30 mins, 45 mins 

488 delay_minutes = attempt * 15 

489 self.logger.debug( 

490 f"Retrying in {delay_minutes}mins ({(datetime.now() + timedelta(minutes=delay_minutes)).time()})", 

491 extra={"url": url}, 

492 ) 

493 time.sleep(delay_minutes * 60) 

494 

495 raise current_exception 

496 

497 def decode_response(self, response: requests.Response, encoding: str | None = None): 

498 """Override this if the content-type headers from the sources are advertising something else than the actual content 

499 SASA needs this""" 

500 # Force 

501 if encoding: 

502 response.encoding = encoding 

503 return response.text 

504 

505 # Attempt to get encoding using HTTP headers 

506 content_type_tag = response.headers.get("Content-Type", None) 

507 

508 if content_type_tag: 508 ↛ 515line 508 didn't jump to line 515 because the condition on line 508 was always true

509 charset = self.parse_content_type_charset(content_type_tag) 

510 if charset: 510 ↛ 511line 510 didn't jump to line 511 because the condition on line 510 was never true

511 response.encoding = charset 

512 return response.text 

513 

514 # Attempt to get encoding using HTML meta charset tag 

515 soup = BeautifulSoup(response.text, "html5lib") 

516 charset = soup.select_one("meta[charset]") 

517 if charset: 

518 htmlencoding = charset.get("charset") 

519 if isinstance(htmlencoding, str): 519 ↛ 524line 519 didn't jump to line 524 because the condition on line 519 was always true

520 response.encoding = htmlencoding 

521 return response.text 

522 

523 # Attempt to get encoding using HTML meta content type tag 

524 content_type_tag = soup.select_one( 

525 'meta[http-equiv="Content-Type"],meta[http-equiv="content-type"]' 

526 ) 

527 if content_type_tag: 

528 content_type = content_type_tag.get("content") 

529 if isinstance(content_type, str): 529 ↛ 535line 529 didn't jump to line 535 because the condition on line 529 was always true

530 charset = self.parse_content_type_charset(content_type) 

531 if charset: 531 ↛ 535line 531 didn't jump to line 535 because the condition on line 531 was always true

532 response.encoding = charset 

533 return response.text 

534 

535 return response.text 

536 

537 @staticmethod 

538 def parse_content_type_charset(content_type: str): 

539 header = EmailPolicy.header_factory("content-type", content_type) 

540 if "charset" in header.params: 

541 return header.params.get("charset") 

542 

543 @tracer.start_as_current_span("add_xissue_to_database") 

544 def add_xissue_into_database(self, xissue: IssueData) -> IssueData: 

545 xissue.journal = self.collection 

546 xissue.source = self.source_domain 

547 

548 if xissue.year == "": 

549 raise ValueError("Failsafe : Cannot insert issue without a year") 

550 

551 xpub = create_publisherdata() 

552 xpub.name = self.publisher 

553 xissue.publisher = xpub 

554 xissue.last_modified_iso_8601_date_str = timezone.now().isoformat() 

555 

556 attempt = 1 

557 success = False 

558 

559 while not success and attempt < 4: 

560 try: 

561 params = {"xissue": xissue, "use_body": False} 

562 cmd = addOrUpdateGDMLIssueXmlCmd(params) 

563 cmd.do() 

564 success = True 

565 self.logger.debug(f"Issue {xissue.pid} inserted in database") 

566 return xissue 

567 except SolrError: 

568 self.logger.warning( 

569 f"Encoutered SolrError while inserting issue {xissue.pid} in database" 

570 ) 

571 attempt += 1 

572 self.logger.debug(f"Attempt {attempt}. sleeping 10 seconds.") 

573 time.sleep(10) 

574 except Exception as e: 

575 self.logger.error( 

576 f"Got exception while attempting to insert {xissue.pid} in database : {e}" 

577 ) 

578 raise e 

579 

580 if success is False: 

581 raise ConnectionRefusedError("Cannot connect to SolR") 

582 

583 assert False, "Unreachable" 

584 

585 def get_metadata_using_citation_meta( 

586 self, 

587 xarticle: ArticleData, 

588 xissue: IssueData, 

589 soup: BeautifulSoup, 

590 what: list[CitationLiteral] = [], 

591 ): 

592 """ 

593 :param xarticle: the xarticle that will collect the metadata 

594 :param xissue: the xissue that will collect the publisher 

595 :param soup: the BeautifulSoup object of tha article page 

596 :param what: list of citation_ items to collect. 

597 :return: None. The given article is modified 

598 """ 

599 

600 if "title" in what: 

601 # TITLE 

602 citation_title_node = soup.select_one("meta[name='citation_title']") 

603 if citation_title_node: 603 ↛ 608line 603 didn't jump to line 608 because the condition on line 603 was always true

604 title = citation_title_node.get("content") 

605 if isinstance(title, str): 605 ↛ 608line 605 didn't jump to line 608 because the condition on line 605 was always true

606 xarticle.title_tex = title 

607 

608 if "author" in what: 608 ↛ 637line 608 didn't jump to line 637 because the condition on line 608 was always true

609 # AUTHORS 

610 citation_author_nodes = soup.select("meta[name^='citation_author']") 

611 current_author: ContributorDict | None = None 

612 for citation_author_node in citation_author_nodes: 

613 if citation_author_node.get("name") == "citation_author": 

614 text_author = citation_author_node.get("content") 

615 if not isinstance(text_author, str): 615 ↛ 616line 615 didn't jump to line 616 because the condition on line 615 was never true

616 raise ValueError("Cannot parse author") 

617 if text_author == "": 617 ↛ 618line 617 didn't jump to line 618 because the condition on line 617 was never true

618 current_author = None 

619 continue 

620 current_author = create_contributor(role="author", string_name=text_author) 

621 xarticle.contributors.append(current_author) 

622 continue 

623 if current_author is None: 623 ↛ 624line 623 didn't jump to line 624 because the condition on line 623 was never true

624 self.logger.warning("Couldn't parse citation author") 

625 continue 

626 if citation_author_node.get("name") == "citation_author_institution": 

627 text_institution = citation_author_node.get("content") 

628 if not isinstance(text_institution, str): 628 ↛ 629line 628 didn't jump to line 629 because the condition on line 628 was never true

629 continue 

630 current_author["addresses"].append(text_institution) 

631 if citation_author_node.get("name") == "citation_author_ocrid": 631 ↛ 632line 631 didn't jump to line 632 because the condition on line 631 was never true

632 text_orcid = citation_author_node.get("content") 

633 if not isinstance(text_orcid, str): 

634 continue 

635 current_author["orcid"] = text_orcid 

636 

637 if "pdf" in what: 

638 # PDF 

639 citation_pdf_node = soup.select_one('meta[name="citation_pdf_url"]') 

640 if citation_pdf_node: 

641 pdf_url = citation_pdf_node.get("content") 

642 if isinstance(pdf_url, str): 642 ↛ 645line 642 didn't jump to line 645 because the condition on line 642 was always true

643 add_pdf_link_to_xarticle(xarticle, pdf_url) 

644 

645 if "lang" in what: 

646 # LANG 

647 citation_lang_node = soup.select_one("meta[name='citation_language']") 

648 if citation_lang_node: 648 ↛ 654line 648 didn't jump to line 654 because the condition on line 648 was always true

649 # TODO: check other language code 

650 content_text = citation_lang_node.get("content") 

651 if isinstance(content_text, str): 651 ↛ 654line 651 didn't jump to line 654 because the condition on line 651 was always true

652 xarticle.lang = standardize_tag(content_text) 

653 

654 if "abstract" in what: 

655 # ABSTRACT 

656 abstract_node = soup.select_one("meta[name='citation_abstract']") 

657 if abstract_node is not None: 

658 abstract = abstract_node.get("content") 

659 if not isinstance(abstract, str): 659 ↛ 660line 659 didn't jump to line 660 because the condition on line 659 was never true

660 raise ValueError("Couldn't parse abstract from meta") 

661 abstract = BeautifulSoup(abstract, "html.parser").text 

662 lang = abstract_node.get("lang") 

663 if not isinstance(lang, str): 

664 lang = self.detect_language(abstract, xarticle) 

665 xarticle.abstracts.append(create_abstract(lang=lang, value_tex=abstract)) 

666 

667 if "page" in what: 

668 # PAGES 

669 citation_fpage_node = soup.select_one("meta[name='citation_firstpage']") 

670 if citation_fpage_node: 

671 page = citation_fpage_node.get("content") 

672 if isinstance(page, str): 672 ↛ 677line 672 didn't jump to line 677 because the condition on line 672 was always true

673 page = page.split("(")[0] 

674 if len(page) < 32: 674 ↛ 677line 674 didn't jump to line 677 because the condition on line 674 was always true

675 xarticle.fpage = page 

676 

677 citation_lpage_node = soup.select_one("meta[name='citation_lastpage']") 

678 if citation_lpage_node: 

679 page = citation_lpage_node.get("content") 

680 if isinstance(page, str): 680 ↛ 685line 680 didn't jump to line 685 because the condition on line 680 was always true

681 page = page.split("(")[0] 

682 if len(page) < 32: 682 ↛ 685line 682 didn't jump to line 685 because the condition on line 682 was always true

683 xarticle.lpage = page 

684 

685 if "doi" in what: 

686 # DOI 

687 citation_doi_node = soup.select_one("meta[name='citation_doi']") 

688 if citation_doi_node: 

689 doi = citation_doi_node.get("content") 

690 if isinstance(doi, str): 690 ↛ 697line 690 didn't jump to line 697 because the condition on line 690 was always true

691 doi = doi.strip() 

692 pos = doi.find("10.") 

693 if pos > 0: 

694 doi = doi[pos:] 

695 xarticle.doi = doi 

696 

697 if "mr" in what: 

698 # MR 

699 citation_mr_node = soup.select_one("meta[name='citation_mr']") 

700 if citation_mr_node: 

701 mr = citation_mr_node.get("content") 

702 if isinstance(mr, str): 702 ↛ 708line 702 didn't jump to line 708 because the condition on line 702 was always true

703 mr = mr.strip() 

704 if mr.find("MR") == 0: 704 ↛ 708line 704 didn't jump to line 708 because the condition on line 704 was always true

705 mr = mr[2:] 

706 xarticle.extids.append(("mr-item-id", mr)) 

707 

708 if "zbl" in what: 

709 # ZBL 

710 citation_zbl_node = soup.select_one("meta[name='citation_zbl']") 

711 if citation_zbl_node: 

712 zbl = citation_zbl_node.get("content") 

713 if isinstance(zbl, str): 713 ↛ 719line 713 didn't jump to line 719 because the condition on line 713 was always true

714 zbl = zbl.strip() 

715 if zbl.find("Zbl") == 0: 715 ↛ 719line 715 didn't jump to line 719 because the condition on line 715 was always true

716 zbl = zbl[3:].strip() 

717 xarticle.extids.append(("zbl-item-id", zbl)) 

718 

719 if "publisher" in what: 

720 # PUBLISHER 

721 citation_publisher_node = soup.select_one("meta[name='citation_publisher']") 

722 if citation_publisher_node: 

723 pub = citation_publisher_node.get("content") 

724 if isinstance(pub, str): 724 ↛ 731line 724 didn't jump to line 731 because the condition on line 724 was always true

725 pub = pub.strip() 

726 if pub != "": 726 ↛ 731line 726 didn't jump to line 731 because the condition on line 726 was always true

727 xpub = create_publisherdata() 

728 xpub.name = pub 

729 xissue.publisher = xpub 

730 

731 if "keywords" in what: 

732 # KEYWORDS 

733 citation_kwd_nodes = soup.select("meta[name='citation_keywords']") 

734 for kwd_node in citation_kwd_nodes: 

735 kwds = kwd_node.get("content") 

736 if isinstance(kwds, str): 736 ↛ 734line 736 didn't jump to line 734 because the condition on line 736 was always true

737 kwds = kwds.split(",") 

738 for kwd in kwds: 

739 if kwd == "": 

740 continue 

741 kwd = kwd.strip() 

742 xarticle.kwds.append({"type": "", "lang": xarticle.lang, "value": kwd}) 

743 

744 if "references" in what: 

745 citation_references = soup.select("meta[name='citation_reference']") 

746 for index, tag in enumerate(citation_references): 

747 content = tag.get("content") 

748 if not isinstance(content, str): 748 ↛ 749line 748 didn't jump to line 749 because the condition on line 748 was never true

749 raise ValueError("Cannot parse citation_reference meta") 

750 label = str(index + 1) 

751 if regex.match(r"^\[\d+\].*", content): 751 ↛ 752line 751 didn't jump to line 752 because the condition on line 751 was never true

752 label = None 

753 xarticle.bibitems.append(self.__parse_meta_citation_reference(content, label)) 

754 

755 def get_metadata_using_dcterms( 

756 self, 

757 xarticle: ArticleData, 

758 soup: "Tag", 

759 what: "Iterable[Literal['abstract', 'keywords', 'date_published', 'article_type']]", 

760 ): 

761 if "abstract" in what: 761 ↛ 769line 761 didn't jump to line 769 because the condition on line 761 was always true

762 abstract_tag = soup.select_one("meta[name='DCTERMS.abstract']") 

763 if abstract_tag: 763 ↛ 769line 763 didn't jump to line 769 because the condition on line 763 was always true

764 abstract_text = self.get_str_attr(abstract_tag, "content") 

765 xarticle.abstracts.append( 

766 create_abstract(lang="en", value_tex=cleanup_str(abstract_text)) 

767 ) 

768 

769 if "keywords" in what: 769 ↛ 778line 769 didn't jump to line 778 because the condition on line 769 was always true

770 keyword_tags = soup.select("meta[name='DC.subject']") 

771 for tag in keyword_tags: 

772 kwd_text = tag.get("content") 

773 if not isinstance(kwd_text, str) or len(kwd_text) == 0: 773 ↛ 774line 773 didn't jump to line 774 because the condition on line 773 was never true

774 continue 

775 kwd = create_subj(value=kwd_text) 

776 xarticle.kwds.append(kwd) 

777 

778 if "date_published" in what: 778 ↛ 779line 778 didn't jump to line 779 because the condition on line 778 was never true

779 published_tag = soup.select_one("meta[name='DC.Date.created']") 

780 if published_tag: 

781 published_text = self.get_str_attr(published_tag, "content") 

782 xarticle.date_published = published_text 

783 

784 if "article_type" in what: 784 ↛ 785line 784 didn't jump to line 785 because the condition on line 784 was never true

785 type_tag = soup.select_one("meta[name='DC.Type.articleType']") 

786 if type_tag: 

787 type_text = self.get_str_attr(type_tag, "content") 

788 xarticle.atype = type_text 

789 

790 def create_xissue( 

791 self, 

792 url: str | None, 

793 year: str, 

794 volume_number: str | None, 

795 issue_number: str | None = None, 

796 vseries: str | None = None, 

797 ): 

798 if url is not None and url.endswith("/"): 

799 url = url[:-1] 

800 xissue = create_issuedata() 

801 xissue.url = url 

802 

803 xissue.pid = self.get_issue_pid( 

804 self.collection_id, year, volume_number, issue_number, vseries 

805 ) 

806 

807 xissue.year = year 

808 

809 if volume_number is not None: 

810 xissue.volume = regex.sub(r"[^\w-]+", "_", volume_number) 

811 

812 if issue_number is not None: 

813 xissue.number = issue_number.replace(",", "-") 

814 

815 if vseries is not None: 815 ↛ 816line 815 didn't jump to line 816 because the condition on line 815 was never true

816 xissue.vseries = vseries 

817 return xissue 

818 

819 def detect_language(self, text: str, article: ArticleData | None = None): 

820 if article and article.lang is not None and article.lang != "und": 

821 return article.lang 

822 

823 language = self.language_detector.detect_language_of(text) 

824 

825 if not language: 825 ↛ 826line 825 didn't jump to line 826 because the condition on line 825 was never true

826 return "und" 

827 return language.iso_code_639_1.name.lower() 

828 

829 def get_str_attr(self, tag: "Tag", attr: str): 

830 """Equivalent of `tag.get(attr)`, but ensures the return value is a string""" 

831 node_attr = tag.get(attr)