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| Author | SHA1 | Date | |
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c57a52e075 | ||
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3fff0bcf0d | ||
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fa4981693c | ||
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3bbcc454c7 | ||
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66a1054472 |
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@@ -96,7 +96,8 @@ class PublicationResult:
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year: int
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pages: Optional[Tuple[int, int]]
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dblp_doi: Optional[str] = None
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authors: List[str] = field(default_factory=list)
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access: Optional[str] = None
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authors: List[Tuple[str,str]] = field(default_factory=list)
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urls: List[str] = field(default_factory=list)
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@property
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@@ -166,7 +167,7 @@ class PublicationResult:
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url = f"https://dblp.uni-trier.de/rec/{key}.xml"
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response = requests.get(url)
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response.raise_for_status
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response.raise_for_status()
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parser = xml.sax.make_parser()
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handler = DBLPHandler({key})
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@@ -195,6 +196,7 @@ class PublicationResult:
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# TODO Parse URLs ('ee')
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doi = None if not 'doi' in info else info['doi']
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access = None if not 'access' in info else info['access']
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return cls(
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key=info['key'],
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@@ -202,7 +204,8 @@ class PublicationResult:
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year=int(info['year']),
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pages=pages,
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dblp_doi=doi,
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authors=[html.unescape(author['text']) for author in authors],
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access = access,
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authors=[(author['@pid'], html.unescape(author['text'])) for author in authors],
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)
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@classmethod
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@@ -223,10 +226,10 @@ class PublicationResult:
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'format': 'json',
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},
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)
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response.raise_for_status
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response.raise_for_status()
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search_result = response.json()['result']
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hits = search_result['hits']
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if hits['@total'] == '0': return (None, None, 0)
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if hits['@total'] == '0' or hits['@sent'] == '0': return (None, None, 0)
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results = [cls.from_search_hit(hit) for hit in hits['hit']]
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total = hits['@total']
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@@ -453,6 +456,7 @@ class Command(BaseCommand):
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# Add authors to database
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authors: List[Author] = []
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for name in result.authors:
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# TODO? find author id's -> not in xml!
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author, created = Author.objects.get_or_create(name=name)
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if created:
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self.log_success(f"Added author: {author}")
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@@ -34,7 +34,7 @@ class Command(BaseCommand):
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self.stdout.write("")
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self.log_info(result.cite_key)
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if 0 < len(result.authors):
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self.stdout.write(" " + ", ".join([name for name in result.authors]))
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self.stdout.write(" " + ", ".join([author.name for author in result.authors]))
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self.log_info(" " + result.title, nl=False)
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self.stdout.write(f" ({result.year})")
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@@ -66,8 +66,16 @@ class Command(BaseCommand):
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# Store Authors
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authors: List[Author] = []
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for name in result.authors:
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for (pid, name) in result.authors:
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author, created = Author.objects.get_or_create(name=name)
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if not author.dblp_id and pid != None:
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try:
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author.dblp_id = pid
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author.full_clean()
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author.save()
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except ValidationError as e:
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raise CommandError(f"{author}: {e}")
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if created:
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self.log_success(f"Added author: {author}")
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else:
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@@ -2,14 +2,19 @@ from pprint import pprint
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from time import sleep
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from tqdm import tqdm
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import re, requests, html
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from django.db import transaction
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from django.core.exceptions import ValidationError
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from django.core.management.base import BaseCommand, CommandError
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from django.core.management.base import BaseCommand, CommandError, CommandParser
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from django.db.models import Count
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from typing import List, Optional, Tuple
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import sok.management.commands.dblpimport as dblp
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from sok.management.commands.snowball import semanticscholar
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from sok.models import Publication, PublicationReference, SemanticScholar
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from sok.models import Publication, PublicationReference, SemanticScholar, Author, PublicationAuthor
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class Command(BaseCommand):
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@@ -17,6 +22,9 @@ class Command(BaseCommand):
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def log_success(self, msg: str):
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self.stdout.write(self.style.SUCCESS(msg))
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def log_warn(self, msg: str):
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self.stdout.write(self.style.WARNING(msg))
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def log_info(self, msg: str, nl: bool = True):
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self.stdout.write(self.style.HTTP_INFO(msg), ending='\n' if nl else '')
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self.stdout.flush()
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@@ -71,6 +79,7 @@ class Command(BaseCommand):
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data = semanticscholar(semantic.paper_id)
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if abstract := data['abstract']:
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publication.abstract = abstract
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if publication.peer_reviewed == None: publication.peer_reviewed = False
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try:
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publication.full_clean()
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publication.save()
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@@ -83,9 +92,22 @@ class Command(BaseCommand):
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def search_on_dblp(self, publication: Publication):
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query, results, total = dblp.PublicationResult.from_search(publication.title, 100)
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if total == 0: return
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plausible = []
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for result in results:
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if publication.doi and result.doi:
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if publication.doi.lower() == result.doi.lower():
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plausible = [result]
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break
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else: continue # quite definitely not the same publication
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elif publication.title == result.title and publication.year == result.year:
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plausible.append(result)
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self.log_warn(f"Not quite certain about {result.cite_key} for publication {publication.title}")
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else: continue # I'd rather look at that in detail for now
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if len(plausible) == 1:
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result = plausible[0]
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if result.access.lower() == 'withdrawn':
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self.log_warn(f"Publication {publication.title} was WITHDRAWN!")
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return
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publication.cite_key = result.cite_key
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publication.year = result.year
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if not result.is_peer_reviewed == None:
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@@ -93,20 +115,56 @@ class Command(BaseCommand):
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publication.first_page = result.first_page
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publication.last_page = result.last_page
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print(publication.peer_reviewed, result)
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# keep authors from semantic scholar for now, even though they might be a little broken?
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try:
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publication.full_clean()
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publication.save()
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self.log_success(f"Added DBLP info for: {publication}")
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except ValidationError as e:
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raise CommandError(f"{publication}: {e}")
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else: continue # quite definitely not the same publication
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elif publication.title == result.title and publication.year == result.year:
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print(f"Not quite certain about {result.cite_key} for publication {publication.title}")
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else: continue # I'd rather look at that in detail for now
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# Store Authors
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authors: List[Author] = []
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for (pid, name) in result.authors:
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author, created = Author.objects.get_or_create(name=name)
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if created:
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self.log_success(f"Added author: {author}")
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else:
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self.log_info(f"Author '{author}' already known")
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if not author.dblp_id and pid != None:
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try:
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author.dblp_id = pid
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author.full_clean()
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author.save()
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self.log_success(f"Added pid to author: {author}")
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except ValidationError as e:
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raise CommandError(f"{author}: {e}")
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authors.append(author)
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# Replace authors for publication
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if len(authors) != len(PublicationAuthor.objects.filter(publication=publication)): print(authors, [pa.author for pa in PublicationAuthor.objects.filter(publication=publication)])
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assert len(authors) >= len(PublicationAuthor.objects.filter(publication=publication))
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for publication_author in PublicationAuthor.objects.filter(publication=publication):
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self.log_warn(f"Will now try to delete {publication_author.author} from {publication}")
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try:
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publication_author.delete()
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except e:
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raise CommandError(f"{publication} - {author}: {e}")
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for position, author in enumerate(authors):
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publication_author, created = PublicationAuthor.objects.get_or_create(
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author=author,
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publication=publication,
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position=position,
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)
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if created:
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self.log_success(f"Assigned author '{author}' to publication '{publication}' at position {position}")
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else:
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self.log_info(f"Author '{author}' already assigned to publication '{publication}' at position '{position}'")
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def find_secondary_on_dblp(self):
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self.log_info("--- Searching for secondary and tertiary sources in the default DBLP dump ---")
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self.log_info("--- Searching for snowballed sources on DBLP ---")
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for publication in tqdm(Publication.objects.exclude(cite_key__startswith=dblp.CITE_KEY_PREFIX), unit="publication"):
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if publication.stage == 'excluded': continue
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self.search_on_dblp(publication)
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@@ -117,7 +175,7 @@ class Command(BaseCommand):
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).values_list('cite_key', flat=True).distinct()
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)
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n = len(keys)
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self.log_info(f"Found {n} publications that still need to be checked")
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self.log_info(f"Found {n} publications that still need to be verified")
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def fix_dblp(self):
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self.log_info("--- Searching for entries not in the default DBLP dump ---")
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@@ -169,12 +227,149 @@ class Command(BaseCommand):
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sleep(2) # Throttle to avoid rate-limiting
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def find_author_on_dblp(
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self,
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name: str,
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limit: int = 100,
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) -> List[Tuple[str, str]]:
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url = 'http://dblp.org/search/author/api'
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response = requests.get(
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url,
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params={
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'q': name,
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'f': 0,
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'h': limit,
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'c': 0,
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'format': 'json',
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},
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)
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response.raise_for_status()
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search_result = response.json()['result']
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hits = search_result['hits']
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if hits['@total'] == '0': return None
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results = [hit['info'] for hit in hits['hit']]
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return results
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def verify_author(self, pid, keys):
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url = f"https://dblp.org/pid/{pid}.xml"
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response = requests.get(url)
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response.raise_for_status()
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pubs = re.findall('key="([^"]*)"', str(response.content))
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sleep(1) # Throttle to avoid rate-limiting
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return keys.intersection(pubs) == keys
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def find_pid_for_authors(self):
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self.log_info("--- Adding ID's to authors ---")
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authors = Author.objects.filter(dblp_id__exact="")
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for author in tqdm(authors, unit='author'):
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pid = ""
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keys = set({
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dblp.strip_cite_key_prefix(cite_key)
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for cite_key in PublicationAuthor.objects.filter(
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author__exact=author,
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publication__cite_key__startswith=dblp.CITE_KEY_PREFIX
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).values_list('publication__cite_key', flat=True).distinct()}
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)
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if len(keys) == 0: continue
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options = self.find_author_on_dblp(author.name)
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if not options:
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self.log_warn(f"Could not find ID for author {author}")
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elif len(options) == 1:
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pid = re.match('https://dblp.org/pid/(.*)', options[0]['url']).groups()[0]
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if self.verify_author(pid, keys):
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self.log_success(f"Found {pid} for author {author}")
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author.dblp_id = pid
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author.full_clean()
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author.save()
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self.log_success(f"Added pid for author {author}")
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else:
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for opt in options:
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if not 'url' in opt: continue
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pid = re.match('https://dblp.org/pid/(.*)', opt['url']).groups()[0]
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if self.verify_author(pid, keys):
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self.log_success(f"Found {pid} for author {author}")
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author.dblp_id = pid
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author.full_clean()
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author.save()
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self.log_success(f"Added pid for author {author}")
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break
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@transaction.atomic
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def merge(self, author, variant):
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for pub_author in PublicationAuthor.objects.filter(author=variant):
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publication = pub_author.publication
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if PublicationAuthor.objects.filter(author=author, publication=publication).exists():
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self.log_warn(f"{author} is already author of {publication}")
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break
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fixed = PublicationAuthor(
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author=author,
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publication=publication,
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position=pub_author.position
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)
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try:
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pub_author.delete()
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fixed.full_clean()
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fixed.save()
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self.log_success(f"Changed author: {publication}: {variant} -> {fixed.author}")
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except ValidationError as e:
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raise CommandError(f"{publication}: {variant} -> {fixed.author}: {e}")
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assert not PublicationAuthor.objects.filter(author=variant).exists()
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variant.delete()
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|
||||
|
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|
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def merge_authors(self) -> None:
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self.log_info("--- Searching for potential duplicate authors and merging their publications ---")
|
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|
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dup_ids = Author.objects.exclude(dblp_id__exact="").values_list('dblp_id').annotate(count=Count('id')).filter(count__gt=1)
|
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|
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try:
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for (pid, counter) in tqdm(dup_ids, unit="duplicate"):
|
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|
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response = requests.get(f"https://dblp.org/pid/{pid}.xml")
|
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response.raise_for_status()
|
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dblp_person = re.search('dblpperson name="([^"]*)"', response.content.decode('ascii')).groups()
|
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assert len(dblp_person) == 1
|
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dblp_name = html.unescape(dblp_person[0])
|
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|
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variants = Author.objects.filter(dblp_id__exact=pid).exclude(name__exact=dblp_name)
|
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# for v in variants:
|
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# print(v.name, v.dblp_id)
|
||||
# break
|
||||
orig = Author.objects.filter(dblp_id__exact=pid, name__exact=dblp_name)
|
||||
print(variants, dblp_name, orig)
|
||||
assert len(orig) == 1
|
||||
|
||||
self.log_info(f"Suggestion to merge {', '.join([v.name for v in variants])} into {orig[0]}")
|
||||
|
||||
while True:
|
||||
self.log_warn("Merge? [Y/n]")
|
||||
choice = input().lower()
|
||||
if choice in {'', 'y', 'yes'}:
|
||||
for variant in variants: self.merge(orig[0], variant)
|
||||
break
|
||||
elif choice in {'', 'n', 'no'}:
|
||||
break
|
||||
except KeyboardInterrupt:
|
||||
raise CommandError("Aborted.")
|
||||
|
||||
# BaseCommand
|
||||
def add_arguments(self, parser: CommandParser):
|
||||
parser.add_argument('-b', '--abstract', action='store_true')
|
||||
parser.add_argument('-d', '--dblp', action='store_true')
|
||||
parser.add_argument('-a', '--authors', action='store_true')
|
||||
parser.add_argument('-s', '--secondary', action='store_true')
|
||||
|
||||
def handle(self, *args, **options):
|
||||
self.fix_references()
|
||||
self.fix_abstracts()
|
||||
self.find_secondary_on_dblp()
|
||||
if options['secondary']: self.find_secondary_on_dblp()
|
||||
if options['dblp']:
|
||||
self.fix_dblp()
|
||||
self.find_missing_dois()
|
||||
self.find_semanticscholar_ids()
|
||||
if options['authors']:
|
||||
self.find_pid_for_authors()
|
||||
self.merge_authors()
|
||||
if options['abstract']: self.fix_abstracts()
|
||||
|
||||
@@ -1,4 +1,8 @@
|
||||
from typing import Set
|
||||
import pickle
|
||||
from django.db.models import Count
|
||||
|
||||
from pathlib import Path
|
||||
|
||||
from django.core.management.base import BaseCommand
|
||||
from django.db.models import Count, Q
|
||||
@@ -43,7 +47,22 @@ class Command(BaseCommand):
|
||||
).distinct():
|
||||
publications_relevant.add(publication.cite_key)
|
||||
|
||||
self.cache_path = Path('.choices.semanticscholar.pickle')
|
||||
if self.cache_path.exists():
|
||||
self.echo("Loading choices from snowballing...")
|
||||
with self.cache_path.open('rb') as f:
|
||||
self.cache = pickle.load(f)
|
||||
self.echo(f"{len(self.cache)} publications excluded during snowballing")
|
||||
self.echo(f"{len(Publication.objects.filter(variant_of__isnull=True))} publications included in total so far")
|
||||
|
||||
# Output
|
||||
self.echo(f"Total publications: {len(publications_found):4d}", bold=True)
|
||||
self.echo(f"- peer reviewed: {len(publications_peer_reviewed):4d}", bold=True)
|
||||
self.echo(f"- relevant: {len(publications_relevant):4d}", bold=True)
|
||||
|
||||
pubs = Publication.objects.values('title').annotate(count=Count('referenced_by')).values('title', 'year', 'count').order_by('count').reverse()
|
||||
for p in pubs[:50]: print(f"{p['title']} ({p['year']}): {p['count']} citations")
|
||||
|
||||
years = Publication.objects.values('year').annotate(count=Count('year')).values('year', 'count')
|
||||
for y in years: print(f"{y['year']}, {y['count']}")
|
||||
|
||||
@@ -0,0 +1,18 @@
|
||||
# Generated by Django 5.2.1 on 2025-05-16 08:36
|
||||
|
||||
from django.db import migrations, models
|
||||
|
||||
|
||||
class Migration(migrations.Migration):
|
||||
|
||||
dependencies = [
|
||||
('sok', '0006_alter_publication_abstract'),
|
||||
]
|
||||
|
||||
operations = [
|
||||
migrations.AddField(
|
||||
model_name='author',
|
||||
name='dblp_id',
|
||||
field=models.CharField(blank=True, max_length=127),
|
||||
),
|
||||
]
|
||||
@@ -7,6 +7,7 @@ from django.db.models.query import QuerySet
|
||||
|
||||
class Author(models.Model):
|
||||
name = models.CharField(max_length=255, unique=True)
|
||||
dblp_id = models.CharField(max_length=127, blank=True)
|
||||
|
||||
def __str__(self) -> str:
|
||||
return self.name
|
||||
|
||||
@@ -0,0 +1,3 @@
|
||||
li a {
|
||||
color: green;
|
||||
}
|
||||
@@ -0,0 +1,21 @@
|
||||
<!doctype html>
|
||||
<html lang="en-US">
|
||||
<head>
|
||||
<meta charset="utf-8" />
|
||||
<title>Tagging publications</title>
|
||||
</head>
|
||||
<body>
|
||||
{% if publication %}
|
||||
{% for author in publication.authors.all %}
|
||||
<a>{{ author.name }}, </a>
|
||||
{% endfor %}
|
||||
<h2>{{ publication.title }} ({{ publication.year }})</h2>
|
||||
{% if publication.doi %}
|
||||
<!-- atm this is a link under /tag as well! -->
|
||||
<a href="https://doi.org/{{ publication.doi }}">{{ publication.doi }}</a>
|
||||
{% endif %}
|
||||
{% else %}
|
||||
<p>No publications are available.</p>
|
||||
{% endif %}
|
||||
</body>
|
||||
</html>
|
||||
@@ -0,0 +1,21 @@
|
||||
<!doctype html>
|
||||
{% load static %}
|
||||
|
||||
<link rel="stylesheet" href="{% static 'tag/style.css' %}">
|
||||
<html lang="en-US">
|
||||
<head>
|
||||
<meta charset="utf-8" />
|
||||
<title>List for tagging publications</title>
|
||||
</head>
|
||||
<body>
|
||||
{% if newest_publications %}
|
||||
<ul>
|
||||
{% for publication in newest_publications %}
|
||||
<li><a href="{% url 'detail' publication.cite_key %}/">{{ publication.title }}, {{publication.year}}</a></li>
|
||||
{% endfor %}
|
||||
</ul>
|
||||
{% else %}
|
||||
<p>No publications are available.</p>
|
||||
{% endif %}
|
||||
</body>
|
||||
</html>
|
||||
@@ -0,0 +1,8 @@
|
||||
from django.urls import path
|
||||
|
||||
from . import views
|
||||
|
||||
urlpatterns = [
|
||||
path("", views.IndexView.as_view(), name="index"),
|
||||
path("<path:cite_key>", views.detail, name="detail"),
|
||||
]
|
||||
+30
-2
@@ -1,3 +1,31 @@
|
||||
from django.shortcuts import render
|
||||
from django.db.models import F
|
||||
from django.http import HttpResponseRedirect
|
||||
from django.shortcuts import get_object_or_404, render
|
||||
from django.urls import reverse
|
||||
from django.views import generic
|
||||
|
||||
from sok.models import Publication, PublicationReference
|
||||
|
||||
|
||||
class IndexView(generic.ListView):
|
||||
template_name = "tag/index.html"
|
||||
context_object_name = "newest_publications"
|
||||
|
||||
def get_queryset(self):
|
||||
return Publication.objects.order_by("-year")[:10]
|
||||
|
||||
def detail(request, cite_key):
|
||||
try:
|
||||
publication = get_object_or_404(Publication, cite_key=cite_key.strip('/'))
|
||||
except Publication.DoesNotExist:
|
||||
raise Http404("Publication does not exist")
|
||||
return render(request, "tag/detail.html", {"publication": publication})
|
||||
|
||||
|
||||
# def overview(request):
|
||||
# try:
|
||||
# ps = Publication.objects.get(...)
|
||||
# except Publication.DoesNotExist:
|
||||
# raise Http404("Publication does not exist")
|
||||
# return render(request, "publications/overview.html", {"to_tag": ps})
|
||||
|
||||
# Create your views here.
|
||||
+2
-1
@@ -14,8 +14,9 @@ Including another URLconf
|
||||
2. Add a URL to urlpatterns: path('blog/', include('blog.urls'))
|
||||
"""
|
||||
from django.contrib import admin
|
||||
from django.urls import path
|
||||
from django.urls import path, include
|
||||
|
||||
urlpatterns = [
|
||||
path('admin/', admin.site.urls),
|
||||
path('tag/', include('sok.urls')),
|
||||
]
|
||||
Reference in new issue
Block a user