Coverage for src/crawler/by_source/msp_crawler.py: 89%
130 statements
« prev ^ index » next coverage.py v7.8.2, created at 2025-06-16 07:44 +0000
1import os
2from urllib.parse import urljoin, urlparse
4from bs4 import BeautifulSoup, Tag
5from ptf.cmds.xml.ckeditor.ckeditor_parser import CkeditorParser
6from ptf.cmds.xml.jats.builder.citation import get_article_title_xml, get_ext_link_xml
7from ptf.cmds.xml.jats.jats_parser import JatsBase
8from ptf.model_data import (
9 ArticleData,
10 create_abstract,
11 create_articledata,
12 create_subj,
13)
15from crawler.base_crawler import BaseCollectionCrawler
16from crawler.utils import cleanup_str, regex_to_dict
19class MspCrawler(BaseCollectionCrawler):
20 source_name = "Mathematical Sciences Publishers"
21 source_domain = "MSP"
22 source_website = "https://msp.org/"
24 issue_re = r"\/\w+\/(?P<year>\d+)\/(?P<volume>\d+)\-(?P<number>\d+)"
26 def parse_collection_content(self, content):
27 xissues = []
28 soup = BeautifulSoup(content, "html.parser")
29 issues = soup.select("td.issues-area a.about[href]")
30 for issue in issues:
31 issue_href = issue.get("href")
32 if not isinstance(issue_href, str): 32 ↛ 33line 32 didn't jump to line 33 because the condition on line 32 was never true
33 raise ValueError("Couldn't parse issue href")
35 issue_dict = regex_to_dict(
36 self.issue_re, issue_href, error_msg="Couldn't parse issue data"
37 )
39 xissues.append(
40 self.create_xissue(
41 urljoin(self.source_website, issue_href),
42 issue_dict["year"],
43 issue_dict["volume"],
44 issue_dict["number"],
45 )
46 )
47 return xissues
49 def parse_issue_content(self, content, xissue):
50 soup = BeautifulSoup(content, "html.parser")
51 if xissue.url is None: 51 ↛ 52line 51 didn't jump to line 52 because the condition on line 51 was never true
52 raise ValueError("Cannot parse article : issue url is None")
54 incomplete = soup.select_one(".incomplete")
55 if incomplete: 55 ↛ 60line 55 didn't jump to line 60 because the condition on line 55 was always true
56 if cleanup_str(incomplete.text) != "Publication of this issue is now complete.": 56 ↛ 57line 56 didn't jump to line 57 because the condition on line 56 was never true
57 print(f"Ignoring {xissue.pid} : Issue is not available due to S2O policy")
58 return
60 issue_doi_tag = soup.select_one("div.issue-doi a")
61 if issue_doi_tag: 61 ↛ 64line 61 didn't jump to line 64 because the condition on line 61 was always true
62 xissue.doi = cleanup_str(issue_doi_tag.text)
64 articles = soup.select("#toc-area .title")
65 for index, article_tag in enumerate(articles):
66 xarticle = create_articledata()
67 article_href = article_tag.get("href")
68 if not isinstance(article_href, str): 68 ↛ 69line 68 didn't jump to line 69 because the condition on line 68 was never true
69 raise ValueError("Couldn't parse article url")
70 xarticle.url = urljoin(xissue.url, article_href)
71 xarticle.pid = "a" + str(index)
72 xissue.articles.append(xarticle)
74 def parse_article_content(self, content, xissue, xarticle, url):
75 soup = BeautifulSoup(content, "html.parser")
77 # Warn : meta doi is sometimes incorrect
78 self.get_metadata_using_citation_meta(
79 xarticle, xissue, soup, ["title", "author", "page", "pdf", "publisher"]
80 )
82 doi_tag = soup.select_one(".paper-doi > a")
83 if doi_tag: 83 ↛ 86line 83 didn't jump to line 86 because the condition on line 83 was always true
84 xarticle.doi = doi_tag.text
86 article_data: dict[str, Tag] = {}
87 article_sections = soup.select("#content-area > .article")
88 for section in article_sections:
89 if section.select_one(".copyright-license"):
90 continue
92 tabs = section.select("tr")
93 section_title_tag = tabs[0].select_one("h5")
94 if not section_title_tag: 94 ↛ 95line 94 didn't jump to line 95 because the condition on line 94 was never true
95 print(f"{xarticle.pid} : Skipping section")
96 continue
97 section_title = section_title_tag.text
98 section_title_tag.decompose()
99 del section_title_tag
101 section_content = tabs[0]
102 if len(tabs) > 1:
103 section_content = tabs[1]
104 section_tag = section_content.select_one("tr > td.article-area")
105 if section_tag: 105 ↛ 88line 105 didn't jump to line 88 because the condition on line 105 was always true
106 article_data[section_title] = section_tag
107 del article_sections
109 if "Keywords" in article_data and article_data["Keywords"] != "": 109 ↛ 113line 109 didn't jump to line 113 because the condition on line 109 was always true
110 for kwd in article_data["Keywords"].text.split(", "):
111 xarticle.kwds.append(create_subj(lang="en", type="kwd", value=kwd))
113 if (
114 "Mathematical Subject Classification 2010" in article_data
115 and article_data["Mathematical Subject Classification 2010"] != ""
116 ):
117 msc_long_text = (
118 cleanup_str(article_data["Mathematical Subject Classification 2010"].text)
119 .replace("Primary: ", "")
120 .replace(" Secondary: ", ", ")
121 )
122 for kwd in msc_long_text.split(", "):
123 xarticle.kwds.append(create_subj(lang="en", type="msc", value=kwd))
125 if "Abstract" in article_data and article_data["Abstract"] != "": 125 ↛ 142line 125 didn't jump to line 142 because the condition on line 125 was always true
126 abstract_str = "".join(str(e) for e in article_data["Abstract"].select("p"))
127 test = CkeditorParser(
128 html_value=abstract_str,
129 mml_formulas="",
130 )
131 # QUESTION : is value_xml here valid, or should we not wrap this inside an abstract tag
132 abstract = create_abstract(
133 lang="en",
134 tag="abstract",
135 value_xml=f'<abstract xml:lang="en">{test.value_xml}</abstract>',
136 value_tex=test.value_tex,
137 value_html=test.value_html,
138 )
140 xarticle.abstracts.append(abstract)
142 self.parse_msp_references(xarticle)
143 return xarticle
145 def parse_msp_references(self, xarticle: ArticleData):
146 url = urlparse(xarticle.url)
147 dirname = os.path.dirname(url.path)
148 filename = os.path.basename(url.path)
149 url = url._replace(path=urljoin(str(dirname) + "/", str(filename).replace("p", "b")))
151 content = self.download_file(str(url.geturl()))
152 soup = BeautifulSoup(content, "html.parser")
153 references = soup.select("#content-area table.article:last-of-type tr")
155 bibitems = []
156 # TODO : extensive parsing (authors, title etc...)
157 # Currently, only the text is inserted
158 for ref in references:
159 td = ref.select("td")
160 value_xml = self.parse_single_ref(td[1])
161 bibitem = JatsBase.bake_ref(value_xml, cleanup_str(td[0].text))
162 bibitems.append(bibitem)
163 if len(bibitems) > 0: 163 ↛ exitline 163 didn't return from function 'parse_msp_references' because the condition on line 163 was always true
164 xarticle.abstracts.append(JatsBase.compile_refs(bibitems))
166 def parse_single_ref(self, tag: Tag):
167 xml_list = []
168 ext_links = []
169 authors_closed = False
171 for element in tag.contents:
172 if isinstance(element, str):
173 xml_list.append(element)
174 continue
175 if isinstance(element, Tag): 175 ↛ 171line 175 didn't jump to line 171 because the condition on line 175 was always true
176 if element.name == "b" and not authors_closed:
177 xml_list.append(f"<string-name>{element.text}</string-name>")
178 elif element.name == "i" and not authors_closed:
179 temp_element = xml_list.pop()
180 xml_list = [
181 f'<person-group person-group-type="author">{cleanup_str("".join(xml_list))}</person-group>',
182 temp_element,
183 ]
184 xml_list.append(get_article_title_xml(element.text))
185 del temp_element
187 link = element.select_one("a")
188 if link:
189 link_href = link.get("href")
190 if isinstance(link_href, str): 190 ↛ 195line 190 didn't jump to line 195 because the condition on line 190 was always true
191 if link_href.startswith("https://doi.org/"):
192 link_href = link_href.removeprefix("https://doi.org/")
193 ext_links.append(get_ext_link_xml(link_href, link_href, "doi"))
195 authors_closed = True
196 elif element.name == "a":
197 pass
198 continue
200 return cleanup_str("".join(xml_list) + "".join(ext_links))