Coverage for src/crawler/by_source/msp_crawler.py: 88%
145 statements
« prev ^ index » next coverage.py v7.8.0, created at 2025-04-24 10:35 +0000
1import os
2from urllib.parse import urljoin, urlparse
4import regex
5from bs4 import BeautifulSoup, Tag
6from ptf.cmds.xml.ckeditor.ckeditor_parser import CkeditorParser
7from ptf.cmds.xml.ckeditor.utils import get_html_and_xml_from_text_with_formulas
8from ptf.cmds.xml.jats.builder.citation import (
9 get_article_title_xml as get_citation_article_title_xml,
10)
11from ptf.cmds.xml.jats.builder.citation import get_ext_link_xml
12from ptf.cmds.xml.jats.builder.issue import get_title_xml as get_issue_title_xml
13from ptf.model_data import (
14 ArticleData,
15 ResourceData,
16 create_abstract,
17 create_articledata,
18 create_subj,
19)
20from ptf.model_data_converter import update_data_for_jats
22from crawler.base_crawler import BaseCollectionCrawler
23from crawler.utils import cleanup_str
26class MspCrawler(BaseCollectionCrawler):
27 source_name = "Mathematical Sciences Publishers"
28 source_domain = "MSP"
29 source_website = "https://msp.org/"
31 issue_re = r"\/\w+\/(?P<year>\d+)\/(?P<volume>\d+)\-(?P<number>\d+)"
33 def parse_collection_content(self, content):
34 xissues = []
35 soup = BeautifulSoup(content, "html.parser")
36 issues = soup.select("td.issues-area a.about[href]")
37 for issue in issues:
38 issue_href = issue.get("href")
39 if not isinstance(issue_href, str): 39 ↛ 40line 39 didn't jump to line 40 because the condition on line 39 was never true
40 raise ValueError("Couldn't parse issue href")
42 issue_search = regex.search(self.issue_re, issue_href)
43 if not issue_search: 43 ↛ 44line 43 didn't jump to line 44 because the condition on line 43 was never true
44 raise ValueError("Couldn't parse issue data")
46 issue_dict = issue_search.groupdict()
48 xissues.append(
49 self.create_xissue(
50 urljoin(self.source_website, issue_href),
51 issue_dict["year"],
52 issue_dict["volume"],
53 issue_dict["number"],
54 )
55 )
56 return xissues
58 def parse_issue_content(self, content, xissue):
59 soup = BeautifulSoup(content, "html.parser")
60 if xissue.url is None: 60 ↛ 61line 60 didn't jump to line 61 because the condition on line 60 was never true
61 raise ValueError("Cannot parse article : issue url is None")
63 incomplete = soup.select_one(".incomplete")
64 if incomplete: 64 ↛ 69line 64 didn't jump to line 69 because the condition on line 64 was always true
65 if cleanup_str(incomplete.text) != "Publication of this issue is now complete.": 65 ↛ 66line 65 didn't jump to line 66 because the condition on line 65 was never true
66 print(f"Ignoring {xissue.pid} : Issue is not available due to S2O policy")
67 return
69 issue_doi_tag = soup.select_one("div.issue-doi a")
70 if issue_doi_tag: 70 ↛ 73line 70 didn't jump to line 73 because the condition on line 70 was always true
71 xissue.doi = cleanup_str(issue_doi_tag.text)
73 articles = soup.select("#toc-area .title")
74 for index, article_tag in enumerate(articles):
75 xarticle = create_articledata()
76 article_href = article_tag.get("href")
77 if not isinstance(article_href, str): 77 ↛ 78line 77 didn't jump to line 78 because the condition on line 77 was never true
78 raise ValueError("Couldn't parse article url")
79 xarticle.url = urljoin(xissue.url, article_href)
80 xarticle.pid = "a" + str(index)
81 xissue.articles.append(xarticle)
83 def parse_article_content(self, content, xissue, xarticle, url):
84 soup = BeautifulSoup(content, "html.parser")
86 # Warn : meta doi is sometimes incorrect
87 self.get_metadata_using_citation_meta(
88 xarticle, xissue, soup, ["title", "author", "page", "pdf", "publisher"]
89 )
91 doi_tag = soup.select_one(".paper-doi > a")
92 if doi_tag: 92 ↛ 95line 92 didn't jump to line 95 because the condition on line 92 was always true
93 xarticle.doi = doi_tag.text
95 article_data: dict[str, Tag] = {}
96 article_sections = soup.select("#content-area > .article")
97 for section in article_sections:
98 if section.select_one(".copyright-license"):
99 continue
101 tabs = section.select("tr")
102 section_title_tag = tabs[0].select_one("h5")
103 if not section_title_tag: 103 ↛ 104line 103 didn't jump to line 104 because the condition on line 103 was never true
104 print(f"{xarticle.pid} : Skipping section")
105 continue
106 section_title = section_title_tag.text
107 section_title_tag.decompose()
108 del section_title_tag
110 section_content = tabs[0]
111 if len(tabs) > 1:
112 section_content = tabs[1]
113 section_tag = section_content.select_one("tr > td.article-area")
114 if section_tag: 114 ↛ 97line 114 didn't jump to line 97 because the condition on line 114 was always true
115 article_data[section_title] = section_tag
116 del article_sections
118 if "Keywords" in article_data and article_data["Keywords"] != "": 118 ↛ 122line 118 didn't jump to line 122 because the condition on line 118 was always true
119 for kwd in article_data["Keywords"].text.split(", "):
120 xarticle.kwds.append(create_subj(lang="en", type="kwd", value=kwd))
122 if (
123 "Mathematical Subject Classification 2010" in article_data
124 and article_data["Mathematical Subject Classification 2010"] != ""
125 ):
126 msc_long_text = (
127 cleanup_str(article_data["Mathematical Subject Classification 2010"].text)
128 .replace("Primary: ", "")
129 .replace(" Secondary: ", ", ")
130 )
131 for kwd in msc_long_text.split(", "):
132 xarticle.kwds.append(create_subj(lang="en", type="msc", value=kwd))
134 if "Abstract" in article_data and article_data["Abstract"] != "": 134 ↛ 151line 134 didn't jump to line 151 because the condition on line 134 was always true
135 abstract_str = "".join(str(e) for e in article_data["Abstract"].select("p"))
136 test = CkeditorParser(
137 html_value=abstract_str,
138 mml_formulas="",
139 )
140 # QUESTION : is value_xml here valid, or should we not wrap this inside an abstract tag
141 abstract = create_abstract(
142 lang="en",
143 tag="abstract",
144 value_xml=f'<abstract xml:lang="en">{test.value_xml}</abstract>',
145 value_tex=test.value_tex,
146 value_html=test.value_html,
147 )
149 xarticle.abstracts.append(abstract)
151 self.parse_msp_references(xarticle)
152 return xarticle
154 def parse_msp_references(self, xarticle: ArticleData):
155 url = urlparse(xarticle.url)
156 dirname = os.path.dirname(url.path)
157 filename = os.path.basename(url.path)
158 url = url._replace(path=urljoin(str(dirname) + "/", str(filename).replace("p", "b")))
160 content = self.download_file(str(url.geturl()))
161 soup = BeautifulSoup(content, "html.parser")
162 references = soup.select("#content-area table.article:last-of-type tr")
164 bibitems = []
165 # TODO : extensive parsing (authors, title etc...)
166 # Currently, only the text is inserted
167 for ref in references:
168 td = ref.select("td")
169 value_xml = self.parse_single_ref(td[1])
170 bibitem = self.create_crawled_bibitem(value_xml, cleanup_str(td[0].text))
171 bibitems.append(bibitem)
172 if len(bibitems) > 0: 172 ↛ exitline 172 didn't return from function 'parse_msp_references' because the condition on line 172 was always true
173 xarticle.abstracts.append(self.create_bibliography(bibitems))
175 def parse_single_ref(self, tag: Tag):
176 xml_list = []
177 ext_links = []
178 authors_closed = False
180 for element in tag.contents:
181 if isinstance(element, str):
182 xml_list.append(element)
183 continue
184 if isinstance(element, Tag): 184 ↛ 180line 184 didn't jump to line 180 because the condition on line 184 was always true
185 if element.name == "b" and not authors_closed:
186 xml_list.append(f"<string-name>{element.text}</string-name>")
187 elif element.name == "i" and not authors_closed:
188 temp_element = xml_list.pop()
189 xml_list = [
190 f'<person-group person-group-type="author">{cleanup_str("".join(xml_list))}</person-group>',
191 temp_element,
192 ]
193 xml_list.append(get_citation_article_title_xml(element.text))
194 del temp_element
196 link = element.select_one("a")
197 if link:
198 link_href = link.get("href")
199 if isinstance(link_href, str): 199 ↛ 204line 199 didn't jump to line 204 because the condition on line 199 was always true
200 if link_href.startswith("https://doi.org/"):
201 link_href = link_href.removeprefix("https://doi.org/")
202 ext_links.append(get_ext_link_xml(link_href, link_href, "doi"))
204 authors_closed = True
205 elif element.name == "a":
206 pass
207 continue
209 return cleanup_str("".join(xml_list) + "".join(ext_links))
211 def process_resource_metadata(self, xresource: ResourceData):
212 html, xml = get_html_and_xml_from_text_with_formulas(
213 xresource.title_tex,
214 delimiter_inline=self.delimiter_inline_formula,
215 delimiter_disp=self.delimiter_disp_formula,
216 )
217 xml = get_issue_title_xml(xml, with_tex_values=False)
218 xresource.title_html = html
219 xresource.title_xml = xml
221 if isinstance(xresource, ArticleData): 221 ↛ 222line 221 didn't jump to line 222 because the condition on line 221 was never true
222 update_data_for_jats(xresource)
224 return xresource