Fix snowballing functionality

sok/management/commands/repair.py

@@ -223,9 +223,10 @@ class Command(BaseCommand):
 				obj.full_clean()
 				obj.save()
 				self.log_success(f"Set semanticscholar ID for publication '{publication}': {paper_id}")
-			else: print(publication)
+			else: 
+				self.log_warn(f"Could not find semanticscholar ID for publication '{publication.title}' with DOI '{publication.doi}'")
 
-			sleep(2)  # Throttle to avoid rate-limiting
+			sleep(1)  # Throttle to avoid rate-limiting (1/s with API Key)
 
 	def find_author_on_dblp(
 		self,
@@ -360,6 +361,7 @@ class Command(BaseCommand):
 		parser.add_argument('-d', '--dblp', action='store_true')
 		parser.add_argument('-a', '--authors', action='store_true')
 		parser.add_argument('-s', '--secondary', action='store_true')
+		parser.add_argument('-i', '--scholarid', action='store_true')
 
 	def handle(self, *args, **options):
 		self.fix_references()
@@ -367,6 +369,7 @@ class Command(BaseCommand):
 		if options['dblp']:
 			self.fix_dblp()
 			self.find_missing_dois()
+		if options['scholarid'] or options['dblp']:
 			self.find_semanticscholar_ids()
 		if options['authors']:
 			self.find_pid_for_authors()

sok/management/commands/snowball.py

@@ -6,6 +6,8 @@ from pathlib import Path
 from time import sleep
 from typing import Any, Dict, List, Set
 
+from django.conf import settings
+
 import requests
 
 from django.core.management.base import BaseCommand, CommandParser, CommandError
@@ -24,7 +26,7 @@ from sok.models import (
 )
 
 
-def semanticscholar(identifier: str, include_unknown_references: bool = False) -> Dict[str, Any]:
+def semanticscholar(identifier: str, fields: str = None, type: str = None, offset: int = 0, include_unknown_references: bool = False) -> Dict[str, Any]:
 	"""
 	Retrieve information from the Semantic Scholar API.
 
@@ -33,11 +35,24 @@ def semanticscholar(identifier: str, include_unknown_references: bool = False) -
 	See: https://api.semanticscholar.org
 	"""
 
-	url = f'https://api.semanticscholar.org/v1/paper/{identifier}'
+	url = f'https://api.semanticscholar.org/graph/v1/paper/{identifier}'
 	params: Dict[str, Any] = dict()
+
+	if type in ['citations', 'references']:
+		url += ('/' + type)
+		params['limit'] = '200'
+		params['offset'] = str(offset)
+
 	if include_unknown_references:
 		params['include_unknown_references'] = 'true'
-	response = requests.get(url, params=params)
+	if fields:
+		params['fields'] = fields
+	
+	headers = {
+			'x-api-key': settings.SCHOLAR_API_KEY
+			}
+
+	response = requests.get(url, params=params, headers=headers)
 	response.raise_for_status
 	return response.json()
 
@@ -48,7 +63,6 @@ class Command(BaseCommand):
 		if bold:
 			msg = self.style.HTTP_INFO(msg)
 		tqdm.write(msg, end='\n' if nl else '')
-		#self.stdout.write(msg, ending='\n' if nl else '')
 
 	def warn(self, msg: str):
 		self.echo(self.style.WARNING(msg))
@@ -113,8 +127,9 @@ class Command(BaseCommand):
 		base: Publication,
 		is_reference: bool,
 	) -> Publication:
-			data = semanticscholar(paper_id)
+			data = semanticscholar(paper_id, fields='title,authors,year,abstract,externalIds')
 			# Add authors to database
+			## TODO: semantic scholar author ids nutzen?
 			authors: List[Author] = []
 			first = True
 			cite_key = ''
@@ -145,7 +160,7 @@ class Command(BaseCommand):
 				publication = None
 
 			# Add publication to database
-			doi = data.get('doi', None)
+			doi = data.get('externalIds', None).get('DOI', None)
 			if not publication:
 				publication = Publication.objects.create(
 					cite_key=cite_key,
@@ -192,9 +207,11 @@ class Command(BaseCommand):
 		title = "Reference" if is_reference else "Citation"
 		if 0 < len(objs):
 			self.echo(f"--- {title}s ---")
-		for obj in tqdm(objs, unit=title.lower()):
+		progress_iterator = tqdm(objs, unit=title.lower(), position=2, leave=False, desc=title + 's')
+		for obj in progress_iterator:
 			if paper_id := obj.get('paperId', None):
 				try:
+					# This publication already exists and has a semantic scholar entry
 					existing = SemanticScholar.objects.get(paper_id=paper_id)
 					if is_reference:
 						self.add_reference(base, existing.publication)
@@ -202,6 +219,7 @@ class Command(BaseCommand):
 						self.add_reference(existing.publication, base, is_reference)
 					continue
 				except SemanticScholar.DoesNotExist:
+					# This publication already exists but does not have a semantic scholar entry
 					if doi := obj.get('doi', None):
 						try:
 							publication = Publication.objects.get(doi=doi)
@@ -215,6 +233,7 @@ class Command(BaseCommand):
 								self.add_reference(new.publication, base, is_reference)
 							continue
 						except Publication.DoesNotExist:
+						# This publication does not exist so we need to create it
 							pass
 
 			identifier = self.get_identifier(obj)
@@ -225,11 +244,12 @@ class Command(BaseCommand):
 
 			paper_id = obj.get('paperId', None)
 			while True:
-				self.echo("Ignore? [Y/n]", nl=True)
-				if paper_id is not None:
+				self.echo("Ignore? [Y/n]", nl=False)
+				if paper_id:
 					self.echo(", Show abstract [a]", nl=False)
 				self.echo(": ")
 				choice = input().lower()
+
 				if choice in {'', 'y', 'yes'}:
 					# Store choice
 					self.cache.add(identifier)
@@ -238,9 +258,10 @@ class Command(BaseCommand):
 					break
 				elif choice in {'a'}:
 					assert paper_id is not None
-					data = semanticscholar(paper_id)
-					if abstract := data.get('abstract', None):
+					if abstract := obj.get('abstract', None):
 						self.echo(abstract)
+					else:
+						self.echo('Sorry, there is no abstract for this publication on Semantic Scholar')
 				elif choice in {'', 'n', 'no'}:
 					# DONE Import? copied and adapted from PR
 					if paper_id is not None:
@@ -277,23 +298,44 @@ class Command(BaseCommand):
 			semanticscholar__isnull=False,
 			exclusion_criteria__isnull=True,
 		)
+
 		if stage < 10000:
 			publications = [p for p in publications if p.stage_added() == stage]
 			self.echo(f"==== {len(publications)} publications from stage {stage} will be shown ====")
 		try:
-			for publication in tqdm(publications, unit="publication"):
+			progress_iterator = tqdm(publications, unit="publication", position=1, desc='Publications')
+			for publication in progress_iterator:
 				self.echo(f"=== Publication {publication}: {publication.title} ===")
 				for semantic in publication.semanticscholar_set.all():
-					data = semanticscholar(semantic.paper_id)
 
 					if not no_references:
-						references: List[Dict[str, Any]] = data['references']
+						offset = 0
+						while True:
+							data = semanticscholar(semantic.paper_id, type='references', fields='title,abstract', offset=offset)
+							if not data.get('data', None):
+								self.echo(self.style.WARNING("API did not return any references, verify manually!"))
+								break
+							references: List[Dict[str, Any]] = [d['citedPaper'] for d in data['data']]
 							self.handle_objs(publication, references, is_reference=True)
+							# Handle limitation if there are more than 200 paper references
+							if 'next' in data: offset = data['next']
+							else: break
 
 					if not no_citations:
-						citations: List[Dict[str, Any]] = data['citations']
+						offset = 0
+						while True:
+							data = semanticscholar(semantic.paper_id, type='citations', fields='title,abstract', offset=offset)
+							if not data.get('data', None):
+								self.echo(self.style.WARNING("API did not return any citations, verify manually!"))
+								break
+							citations: List[Dict[str, Any]] = [d['citingPaper'] for d in data['data']]
 							self.handle_objs(publication, citations, is_reference=False)
+							# Handle limitation if there are more than 200 paper references
+							if 'next' in data: offset = data['next']
+							else: break
+
+					sleep(1)  # Throttle
 
-					sleep(2)  # Throttle
 		except KeyboardInterrupt:
 			raise CommandError("Aborted.")
+

sok/management/commands/zimport.py

@@ -0,0 +1,154 @@
+import html
+import io
+import string
+import csv
+
+from dataclasses import dataclass, field
+from datetime import datetime
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Set, Tuple, Union
+
+import requests
+
+from django.db import transaction
+from django.core.management.base import BaseCommand, CommandParser, CommandError
+
+from sok.models import (
+	Author,
+	Publication,
+	PublicationAuthor,
+	PublicationSource,
+	PublicationTag,
+	SearchTerm,
+	Source,
+	Tag,
+)
+
+
+
+# TODO: anpassen für WoS?
+PUBLICATIONS = {
+	'article',
+	'inproceedings',
+	'proceedings',
+	'book',
+	'incollection',
+	'phdthesis',
+	'mastersthesis',
+	'www',
+	'person',
+	'data',
+}
+
+CITE_KEY_PREFIX = 'Z:'
+
+
+class Command(BaseCommand):
+
+	def log_success(self, msg: str):
+		self.stdout.write(self.style.SUCCESS(msg))
+
+	def log_info(self, msg: str, nl: bool = True):
+		self.stdout.write(self.style.HTTP_INFO(msg), ending='\n' if nl else '')
+		self.stdout.flush()
+
+	# BaseCommand
+
+	def add_arguments(self, parser: CommandParser):
+		parser.add_argument('--search-term', default='Not specified')
+		parser.add_argument('--source', default='Zotero')
+		parser.add_argument('zfile')
+
+	@transaction.atomic
+	def handle(self, *args, **options):
+		source, created = Source.objects.get_or_create(name=options['source'])
+
+		search_term: Optional[SearchTerm] = None
+		if name := options['search_term']:
+			search_term, created = SearchTerm.objects.get_or_create(name=name)
+			if created:
+				self.log_success(f"Created search term: {search_term}")
+
+		publications: List[Publication] = []
+
+		zotero_file = options['zfile']
+		with open(zotero_file, 'r') as csvfile:
+			reader = csv.DictReader(csvfile)
+			for publ in reader:
+
+				authors: List[Author] = []
+				for name in set(publ['Author'].split('; ')):
+					author, created = Author.objects.get_or_create(name=name)
+					if created:
+						self.log_success(f"Added author: {author}")
+					else:
+						self.log_info(f"Author '{author}' already known")
+					authors.append(author)
+
+				tags: List[Tag] = []
+				for t in set(publ['Manual Tags'].split('; ')).union(publ['Automatic Tags'].split('; ')):
+					if t == '': continue
+					tag, created = Tag.objects.get_or_create(name=t)
+					if created:
+						self.log_success(f"Added tag: {tag}")
+					else:
+						self.log_info(f"Tag '{tag}' already exists")
+					tags.append(tag)
+
+				pages = (None, None)
+				if '-' in publ['Pages']: 
+					pages = publ['Pages'].split('-')
+
+				# Add publication to database
+				publication, created = Publication.objects.get_or_create(
+					cite_key=publ['Key'],
+					title=publ['Title'],
+					year=publ['Publication Year'],
+					# TODO: peer_reviewed=result.is_peer_reviewed,
+					first_page=pages[0],
+					last_page=pages[1],
+					doi=publ['DOI'] or None,
+					abstract=publ['Abstract Note'] or None,
+				)
+				if created:
+					self.log_success(f"Added publication: {publication}")
+				else:
+					self.log_info(f"Publication '{publication}' already known")
+				publications.append(publication)
+
+				# Assign authors
+				for position, author in enumerate(authors):
+					publication_author, created = PublicationAuthor.objects.get_or_create(
+						author=author,
+						publication=publication,
+						position=position,
+					)
+					if created:
+						self.log_success(f"Assigned author '{author}' to publication '{publication}' at position {position}")
+					else:
+						self.log_info(f"Author '{author}' already assigned to publication '{publication}' at position '{position}'")
+
+				# Assign tags
+				for position, tag in enumerate(tags):
+					publication_tag, created = PublicationTag.objects.get_or_create(
+						tag=tag,
+						publication=publication,
+					)
+					if created:
+						self.log_success(f"Assigned tag '{tag}' to publication '{publication}'")
+					else:
+						self.log_info(f"Tag '{tag}' already assigned to publication '{publication}'")
+
+		# Assign sources
+		if search_term is not None:
+			for publication in publications:
+				print(publication, search_term, source)
+				publication_source, created = PublicationSource.objects.get_or_create(
+					source=source,
+					publication=publication,
+					search_term=search_term,
+				)
+				if created:
+					self.log_success(f"Assigned source '{source}' to publication '{publication}' with search term '{search_term}'")
+				else:
+					self.log_info(f"Source '{source}' already assigned to publication '{publication}' with search term '{search_term}'")

sokman/settings.py

@@ -32,9 +32,17 @@ def get_or_generate_key() -> str:
 	assert path.exists()
 	return path.read_text()
 
+def get_api_key() -> str:
+	path = Path(Path(__file__).parent,'api.secret')
+
+	assert path.exists()
+	return path.read_text()
+
 # SECURITY WARNING: keep the secret key used in production secret!
 SECRET_KEY = get_or_generate_key()
 
+SCHOLAR_API_KEY = get_api_key().strip('\n')
+
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = True
 
@@ -89,9 +97,13 @@ WSGI_APPLICATION = 'sokman.wsgi.application'
 
 DATABASES = {
 	'default': {
+		'ENGINE': 'django.db.backends.sqlite3',
+		'NAME': BASE_DIR / 'jens.sqlite3',
+	},
+	'uc_sok': {
 		'ENGINE': 'django.db.backends.sqlite3',
 		'NAME': BASE_DIR / 'db.sqlite3',
-	}
+	},
 }