From eced4f377eed3d629530303a80575a9292f0cbf4 Mon Sep 17 00:00:00 2001 From: mskarlin <12701035+mskarlin@users.noreply.github.com> Date: Wed, 14 Aug 2024 14:02:03 -0700 Subject: [PATCH] Add Client (external API) Module For Enhanced Metadata (#306) * first pass at adding clients module * remove settings.py * add client module and holder docdetails type * remove some TODOs and add weird request test * stop pulling bibtex if not requested * better comment on bibtex usage * fix eof error * revert to default email for test cassettes * s2 and crossref module-level api headers * move doi_url into its own field, refactor all model validators into one method, regenerate all cassettes with new fields * add robustness for timeout errors * move exception handling into parent method * add explicit "prefer other" to the __add__ method and use crossref in live tests for stability * move clients/utils into utils * rename text in prompt to citation * use loop in tests * adjust citation prompt, add docstring for populate_bibtex_key_citation, replace bibtex extract w pattern, lower timeout threshold in test * add topological run-order via nested sequence --------- Co-authored-by: Michael Skarlinski --- .pre-commit-config.yaml | 9 + dev-requirements.txt | 1 + paperqa/__init__.py | 2 + paperqa/clients/__init__.py | 177 + .../clients/client_data/journal_quality.csv | 39358 ++++++++++++++++ paperqa/clients/client_models.py | 166 + paperqa/clients/crossref.py | 344 + paperqa/clients/exceptions.py | 4 + paperqa/clients/journal_quality.py | 57 + paperqa/clients/semantic_scholar.py | 319 + paperqa/docs.py | 77 +- paperqa/prompts.py | 8 + paperqa/types.py | 388 +- paperqa/utils.py | 229 +- pyproject.toml | 1 + tests/.gitignore | 3 + tests/cassettes/test_author_matching.yaml | 195 + tests/cassettes/test_bad_dois.yaml | 87 + tests/cassettes/test_bad_titles.yaml | 333 + tests/cassettes/test_bulk_doi_search.yaml | 1322 + tests/cassettes/test_bulk_title_search.yaml | 1404 + ...ssref_journalquality_fields_filtering.yaml | 52 + .../test_doi_search[paper_attributes0].yaml | 199 + .../test_doi_search[paper_attributes1].yaml | 158 + .../test_doi_search[paper_attributes2].yaml | 154 + .../cassettes/test_ensure_sequential_run.yaml | 136 + ...test_ensure_sequential_run_early_stop.yaml | 91 + .../test_minimal_fields_filtering.yaml | 135 + tests/cassettes/test_odd_client_requests.yaml | 545 + .../test_s2_only_fields_filtering.yaml | 96 + .../test_title_search[paper_attributes0].yaml | 248 + .../test_title_search[paper_attributes1].yaml | 196 + .../test_title_search[paper_attributes2].yaml | 470 + tests/conftest.py | 17 + tests/test_clients.py | 489 + tests/test_paperqa.py | 43 + 36 files changed, 47507 insertions(+), 6 deletions(-) create mode 100644 paperqa/clients/__init__.py create mode 100644 paperqa/clients/client_data/journal_quality.csv create mode 100644 paperqa/clients/client_models.py create mode 100644 paperqa/clients/crossref.py create mode 100644 paperqa/clients/exceptions.py create mode 100644 paperqa/clients/journal_quality.py create mode 100644 paperqa/clients/semantic_scholar.py create mode 100644 tests/.gitignore create mode 100644 tests/cassettes/test_author_matching.yaml create mode 100644 tests/cassettes/test_bad_dois.yaml create mode 100644 tests/cassettes/test_bad_titles.yaml create mode 100644 tests/cassettes/test_bulk_doi_search.yaml create mode 100644 tests/cassettes/test_bulk_title_search.yaml create mode 100644 tests/cassettes/test_crossref_journalquality_fields_filtering.yaml create mode 100644 tests/cassettes/test_doi_search[paper_attributes0].yaml create mode 100644 tests/cassettes/test_doi_search[paper_attributes1].yaml create mode 100644 tests/cassettes/test_doi_search[paper_attributes2].yaml create mode 100644 tests/cassettes/test_ensure_sequential_run.yaml create mode 100644 tests/cassettes/test_ensure_sequential_run_early_stop.yaml create mode 100644 tests/cassettes/test_minimal_fields_filtering.yaml create mode 100644 tests/cassettes/test_odd_client_requests.yaml create mode 100644 tests/cassettes/test_s2_only_fields_filtering.yaml create mode 100644 tests/cassettes/test_title_search[paper_attributes0].yaml create mode 100644 tests/cassettes/test_title_search[paper_attributes1].yaml create mode 100644 tests/cassettes/test_title_search[paper_attributes2].yaml create mode 100644 tests/conftest.py create mode 100644 tests/test_clients.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d8781cee..bc5f44bb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -5,6 +5,10 @@ repos: rev: v4.6.0 hooks: - id: check-added-large-files + exclude: | + (?x)^( + paperqa/clients/client_data.* + )$ - id: check-byte-order-marker - id: check-case-conflict - id: check-merge-conflict @@ -50,6 +54,11 @@ repos: hooks: - id: codespell additional_dependencies: [".[toml]"] + exclude: | + (?x)^( + tests/cassettes.*| + paperqa/clients/client_data.* + )$ - repo: https://github.com/abravalheri/validate-pyproject rev: v0.18 hooks: diff --git a/dev-requirements.txt b/dev-requirements.txt index 1350e5ac..a2f226af 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -16,6 +16,7 @@ pre-commit pytest pytest-asyncio pytest-sugar +pytest-vcr pytest-timer types-requests types-setuptools diff --git a/paperqa/__init__.py b/paperqa/__init__.py index 2de2ce63..d4291b30 100644 --- a/paperqa/__init__.py +++ b/paperqa/__init__.py @@ -18,6 +18,7 @@ llm_model_factory, vector_store_factory, ) +from .types import DocDetails from .version import __version__ __all__ = [ @@ -25,6 +26,7 @@ "AnthropicLLMModel", "Context", "Doc", + "DocDetails", "Docs", "EmbeddingModel", "HybridEmbeddingModel", diff --git a/paperqa/clients/__init__.py b/paperqa/clients/__init__.py new file mode 100644 index 00000000..e3956f98 --- /dev/null +++ b/paperqa/clients/__init__.py @@ -0,0 +1,177 @@ +from __future__ import annotations + +import copy +import logging +from typing import Any, Collection, Coroutine, Sequence + +import aiohttp +from pydantic import BaseModel, ConfigDict + +from ..types import Doc, DocDetails +from ..utils import gather_with_concurrency +from .client_models import MetadataPostProcessor, MetadataProvider +from .crossref import CrossrefProvider +from .journal_quality import JournalQualityPostProcessor +from .semantic_scholar import SemanticScholarProvider + +logger = logging.getLogger(__name__) + +ALL_CLIENTS: ( + Collection[type[MetadataPostProcessor | MetadataProvider]] + | Sequence[Collection[type[MetadataPostProcessor | MetadataProvider]]] +) = { + CrossrefProvider, + SemanticScholarProvider, + JournalQualityPostProcessor, +} + + +class DocMetadataTask(BaseModel): + """Holder for provider and processor tasks.""" + + providers: Collection[MetadataProvider] + processors: Collection[MetadataPostProcessor] + + model_config = ConfigDict(arbitrary_types_allowed=True) + + def provider_queries( + self, query: dict + ) -> list[Coroutine[Any, Any, DocDetails | None]]: + return [p.query(query) for p in self.providers] + + def processor_queries( + self, doc_details: DocDetails, session: aiohttp.ClientSession + ) -> list[Coroutine[Any, Any, DocDetails]]: + return [ + p.process(copy.copy(doc_details), session=session) for p in self.processors + ] + + def __repr__(self) -> str: + return ( + f"DocMetadataTask(providers={self.providers}, processors={self.processors})" + ) + + +class DocMetadataClient: + def __init__( + self, + session: aiohttp.ClientSession | None = None, + clients: ( + Collection[type[MetadataPostProcessor | MetadataProvider]] + | Sequence[Collection[type[MetadataPostProcessor | MetadataProvider]]] + ) = ALL_CLIENTS, + ) -> None: + """Metadata client for querying multiple metadata providers and processors. + + Args: + session: outer scope aiohttp session to allow for connection pooling + clients: list of MetadataProvider and MetadataPostProcessor classes to query; + if nested, will query in order looking for termination criteria after each. + Will terminate early if either DocDetails.is_hydration_needed is False OR if + all requested fields are present in the DocDetails object. + + """ + self._session = session + self.tasks: list[DocMetadataTask] = [] + + # first see if we are nested; i.e. we want order + if isinstance(clients, Sequence) and all( + isinstance(sub_clients, Collection) for sub_clients in clients + ): + for sub_clients in clients: + self.tasks.append( + DocMetadataTask( + providers=[ + c() for c in sub_clients if issubclass(c, MetadataProvider) + ], + processors=[ + c() + for c in sub_clients + if issubclass(c, MetadataPostProcessor) + ], + ) + ) + # otherwise, we are a flat collection + if not self.tasks and all(not isinstance(c, Collection) for c in clients): + self.tasks.append( + DocMetadataTask( + providers=[c() for c in clients if issubclass(c, MetadataProvider)], # type: ignore[operator, arg-type] + processors=[ + c() for c in clients if issubclass(c, MetadataPostProcessor) # type: ignore[operator, arg-type] + ], + ) + ) + + if not self.tasks or (self.tasks and not self.tasks[0].providers): + raise ValueError("At least one MetadataProvider must be provided.") + + async def query(self, **kwargs) -> DocDetails | None: + + session = aiohttp.ClientSession() if self._session is None else self._session + + query_args = kwargs if "session" in kwargs else kwargs | {"session": session} + + doc_details: DocDetails | None = None + + for ti, task in enumerate(self.tasks): + logger.debug( + f"Attempting to populate metadata query: {query_args} via {task}" + ) + + # first query all client_models and aggregate the results + doc_details = ( + sum( + p + for p in ( + await gather_with_concurrency( + len(task.providers), task.provider_queries(query_args) + ) + ) + if p + ) + or None + ) + + # then process and re-aggregate the results + if doc_details and task.processors: + doc_details = sum( + await gather_with_concurrency( + len(task.processors), + task.processor_queries(doc_details, session), + ) + ) + + if doc_details and not doc_details.is_hydration_needed( + inclusion=kwargs.get("fields", []) + ): + logger.debug( + "All requested fields are present in the DocDetails " + f"object{', stopping early.' if ti != len(self.tasks) - 1 else '.'}" + ) + break + + return doc_details + + async def bulk_query( + self, queries: Collection[dict[str, Any]], concurrency: int = 10 + ) -> list[DocDetails]: + return await gather_with_concurrency( + concurrency, [self.query(**kwargs) for kwargs in queries] + ) + + async def upgrade_doc_to_doc_details(self, doc: Doc, **kwargs) -> DocDetails: + if doc_details := await self.query(**kwargs): + if doc.overwrite_fields_from_metadata: + return doc_details + # hard overwrite the details from the prior object + doc_details.dockey = doc.dockey + doc_details.doc_id = doc.dockey + doc_details.docname = doc.docname + doc_details.key = doc.docname + doc_details.citation = doc.citation + return doc_details + + # if we can't get metadata, just return the doc, but don't overwrite any fields + prior_doc = doc.model_dump() + prior_doc["overwrite_fields_from_metadata"] = False + return DocDetails(**prior_doc) diff --git a/paperqa/clients/client_data/journal_quality.csv b/paperqa/clients/client_data/journal_quality.csv new file mode 100644 index 00000000..e3b4900f --- /dev/null +++ b/paperqa/clients/client_data/journal_quality.csv @@ -0,0 +1,39358 @@ +clean_name,quality +francke verlag,1 +aaai press,1 +aalborg university press,1 +aalto arts books,1 +aarhus university press,1 +abc-clio,0 +abilene christian university press,1 +abstrakt forlag,1 +academia adacta,1 +academia press,1 +academic press,2 +academica,1 +accademia nazionale dei lincei,1 +acco,1 +academic conferences international,1 +acoustical society of america,0 +acta graphica publishers,0 +acta press,1 +actes sud,1 +acton publishers,1 +acumen,1 +addis ababa university press,1 +adonis & abbey publishers ltd.,1 +advanced knowledge international,1 +africa institute of south africa,1 +africa world press,1 +associazione italiana di ingegneria chimica,1 +aisthesis verlag,1 +akadémiai kiadó,1 +"akademie der wissenschaften und der literatur, mainz",1 +akademie der wissenschaften zu göttingen,1 +akademie verlag,1 +akademisk forlag,1 +akademisk publisering,1 +akashi shoten,1 +akilles forlag,1 +aletejja,1 +alfred kröner,1 +allen & unwin,1 +allied publishers group,1 +almenna bókafélagið,1 +almqvist & wiksell,1 +alpha science international,1 +altamira press,2 +alvheim & eide,1 +american association for the advancement of science,1 +american association of petroleum geologists,1 +american center for oriental research,1 +american ceramic society,1 +american chemical society,2 +american concrete institute,1 +american geophysical union,1 +american historical association,1 +american institute of aeronautics and astronautics,1 +american institute of biological sciences,1 +american institute of chemical engineers,1 +american 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research journal,1 +clues: a journal of detection,1 +cluster computing: the journal of networks software tools and applications,1 +"computers, materials & continua",1 +cmes: computer modeling in engineering and sciences,1 +cns and neurological disorders-drug targets,1 +cns drugs,1 +cns neuroscience and therapeutics,1 +cns spectrums,1 +coaching psychologist,1 +coastal engineering,3 +coastal engineering journal,1 +coastal management,1 +cochrane database of systematic reviews,2 +codesign: international journal of cocreation in design and the arts,3 +codices manuscripti: zeitschrift für handschriftenkunde,1 +cogito,1 +cognitextes,1 +cognitio: revista de filosofia,1 +cognition,3 +cognition and emotion,2 +cognition and instruction,2 +"cognition, technology and work",1 +cognitive affective and behavioral neuroscience,1 +cognitive and behavioral neurology,1 +cognitive and behavioral practice,1 +cognitive development,1 +cognitive linguistics,3 +cognitive neurodynamics,1 +cognitive 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industries,1 +competition policy international,1 +complementary therapies in clinical practice,1 +complementary therapies in medicine,1 +complex analysis and operator theory,1 +complex variables and elliptic equations,1 +complexity,1 +composite interfaces,1 +composite structures,2 +composites part a: applied science and manufacturing,2 +composites part b: engineering,3 +composites science and technology,2 +compositio mathematica,2 +compost science and utilization,1 +comprehensive psychiatry,2 +comprehensive reviews in food science and food safety,2 +comprehensive therapy,1 +compstat,1 +comptes rendus biologies,1 +comptes rendus chimie,0 +comptes rendus des seances de lacademie des inscriptions et belles-lettres,1 +comptes rendus geoscience,1 +comptes rendus mathematique,1 +comptes rendus mecanique,1 +comptes rendus palevol,1 +comptes rendus physique,1 +computational and applied mathematics,1 +computational and mathematical methods in medicine,0 +computational and mathematical 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computer communications and networks,1 +computer fraud and security,1 +computer graphics forum,1 +proceedings : computer graphics international,1 +computer graphics world,1 +computer journal,1 +computer languages systems and structures,1 +computer law & security review,1 +computer methods and programs in biomedicine,1 +computer methods in applied mechanics and engineering,3 +computer methods in biomechanics and biomedical engineering,1 +computer music journal,3 +computer networks,2 +computer physics communications,1 +computer science and information systems,1 +computer science and telecommunications,1 +computer science education,2 +computer science review,1 +computer speech and language,2 +computer standards and interfaces,1 +computer-supported collaborative learning,1 +computer supported cooperative work: the journal of collaborative computing,3 +computer systems science and engineering,1 +computer vision and image understanding,2 +computer-aided civil and infrastructure engineering,3 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and transformation,1 +concepts in magnetic resonance part a,1 +concepts in magnetic resonance part b: magnetic resonance engineering,1 +concilium medii aevi,1 +concilium: international journal of theology,1 +concordia theological quarterly,1 +concrete international,1 +concurrency and computation: practice and experience,1 +concurrent engineering: research and applications,1 +condensed matter physics,1 +conference on uncertainty in artificial intelligence,2 +theoretical aspects of rationality and knowledge,1 +conference proceedings : international conference on indium phosphide and related materials,1 +"ieee international conference on systems, man, and cybernetics",1 +conference record of the industry applications society annual meeting,1 +conference record of the ieee photovoltaic specialists conference,1 +configurations,1 +conflict and communication,1 +conflict management and peace science,2 +conflict resolution quarterly,1 +"conflict, security and development",1 +confluencia: revista hispanica de cultura y literatura,1 +conformal geometry and dynamics,1 +confrontation,1 +congenital anomalies,1 +congenital heart disease,1 +congressus internationalis fenno-ugristarum,1 +connaissance des arts,1 +connect: the world of critical care nursing,1 +connection science,1 +connective tissue research,1 +connotations: a journal for critical debate,1 +conradian,1 +conradiana,1 +consciousness and emotion,1 +consciousness and cognition,2 +"consciousness, literature and the arts",1 +conservation and management of archaeological sites,2 +conservation and society,2 +conservation biology,3 +conservation genetics,1 +conservation letters,3 +constellations: an international journal of critical and democratic theory,1 +constitutional commentary,1 +constitutional law library,1 +constitutional political economy,1 +constraints,1 +construction and building materials,1 +construction history,1 +construction management and economics,1 +constructions,1 +constructions and frames,2 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nurse,1 +contemporary ob/gyn,1 +contemporary pacific,2 +contemporary physics,1 +contemporary political theory,2 +contemporary politics,1 +contemporary pragmatism,1 +contemporary problems of ecology,1 +contemporary psychoanalysis,1 +contemporary security policy,1 +contemporary sociology: a journal of reviews,1 +contemporary south asia,2 +contemporary theatre review,3 +contemporary womens writing,1 +contexts,1 +continental philosophy review,3 +continental shelf research,1 +continuity and change,2 +continuum mechanics and thermodynamics,1 +continuum: journal of media and cultural studies,1 +contraception,1 +contrast media and molecular imaging,0 +contrastes: revista interdisciplinar de filosofia,1 +contributions of the austrian ludwig wittgenstein society,1 +contributions to indian sociology,2 +contributions to mineralogy and petrology,2 +contributions to music education,1 +contributions to nephrology,1 +contributions to phenomenology,2 +contributions to plasma physics,1 +contributions to political economy,1 +contributions to zoology,1 +control and cybernetics,1 +control engineering and applied informatics,1 +control engineering practice,2 +control solutions international,1 +controversies,1 +convergence: the international journal of research into new media technologies,2 +convergencia: revista de ciencias sociales,1 +converging evidence in language and communication research,1 +conveyancer and property lawyer,1 +convivium: revista de filosofia,1 +international conference on the design of cooperative systems,1 +cooperation and conflict,2 +coordination chemistry reviews,1 +copd : journal of chronic obstructive pulmonary disease,1 +copenhagen journal of asian studies,1 +copenhagen studies in language,1 +coptica,1 +coral reefs,1 +core: conservation et restauration du patrimoine cultural,1 +cornea,1 +cornell hospitality quarterly,1 +cornell international law journal,1 +cornell journal of law and public policy,1 +cornell law review,2 +cornish archaeology,1 +coronary artery disease,1 +"la corónica: a journal of medieval hispanic languages, literatures, and cultures",1 +corpora,1 +"corporate board: role, duties and composition",1 +corporate communications,1 +corporate governance: the international journal of business in society,1 +corporate governance: an international review,2 +corporate reputation review,1 +corporate social responsibility and environmental management,1 +corpus linguistics and linguistic theory,3 +correspondances en mhnd,1 +corrosion,1 +corrosion engineering science and technology,1 +corrosion reviews,1 +corrosion science,3 +cortex,2 +cosmic research,1 +cosmos and history: the journal of natural and social philosophy,1 +cost effectiveness and resource allocation,1 +costume,1 +counseling and values,1 +counseling psychologist,1 +counselling and psychotherapy research,1 +counselling psychology quarterly,1 +counselor education and supervision,1 +craft research,2 +cranio,1 +crearta: the international journal of the education in the arts,1 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atherosclerosis reports,1 +current bioactive compounds,1 +current bioinformatics,1 +current biology,3 +current cancer drug targets,1 +current cardiology reports,1 +current chemical biology,1 +current computer-aided drug design,1 +current diabetes reports,1 +current directions in psychological science,2 +current drug delivery,1 +current drug discovery technologies,1 +current drug metabolism,1 +current drug targets,1 +current drug therapy,1 +current enzyme inhibition,1 +current eye research,1 +current gene therapy,1 +current genetics,1 +current genomics,1 +current history,1 +current hiv research,1 +current hypertension reports,1 +current infectious disease reports,1 +current issues in comparative education,1 +current issues in education,1 +current issues in language planning,1 +current issues in molecular biology,1 +current issues in tourism,2 +current legal problems,2 +current medical imaging reviews,1 +current medical research and opinion,1 +current medicinal chemistry,1 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opinion in molecular therapeutics,1 +current opinion in nephrology and hypertension,1 +current opinion in neurobiology,1 +current opinion in neurology,1 +current opinion in obstetrics and gynecology,1 +current opinion in oncology,1 +current opinion in ophthalmology,1 +current opinion in organ transplantation,1 +current opinion in otolaryngology and head and neck surgery,1 +current opinion in pediatrics,1 +current opinion in pharmacology,1 +current opinion in plant biology,1 +current opinion in psychiatry,1 +current opinion in pulmonary medicine,1 +current opinion in rheumatology,1 +current opinion in solid state and materials science,2 +current opinion in structural biology,1 +current opinion in urology,1 +current organic chemistry,1 +current organic synthesis,1 +current pain and headache reports,1 +current pharmaceutical analysis,1 +current pharmaceutical biotechnology,1 +current pharmaceutical design,1 +current politics and economics of europe,1 +current problems in cancer,1 +current problems in cardiology,1 +current problems in dermatology,1 +current problems in diagnostic radiology,1 +current problems in surgery,1 +current protein and peptide science,1 +current proteomics,1 +current psychiatry reports,1 +current psychology,1 +"current psychology letters: behaviour, brain and cognition",1 +current research in social psychology,1 +current rheumatology reviews,1 +current signal transduction therapy,1 +current sociology,2 +current sports medicine reports,1 +current stem cell research and therapy,1 +current swedish archaeology,1 +current therapeutic research: clinical and experimental,1 +current topics in developmental biology,1 +current topics in medicinal chemistry,1 +current topics in membranes,1 +current topics in microbiology and immunology,1 +current treatment options in neurology,1 +current treatment options in oncology,1 +current vascular pharmacology,1 +current womens health reviews,1 +current writing : text and reception in southern africa,1 +current zoology,1 +currents in biblical research,1 +curriculum and teaching,1 +curriculum inquiry,1 +curriculum journal,2 +curriculum matters,1 +custos e agronegócio,1 +cutaneous and ocular toxicology,1 +cutis,1 +cw3 journal: corvey women writers on the web,1 +cybergeo,1 +cybermetrics,1 +"cybernetics and human knowing: a journal of second order cybernetics, autopoiesis and cyber-semiotics",1 +cybernetics and information technologies,1 +cybernetics and systems,1 +cybernetics and systems analysis,1 +cyberpsychology behavior and social networking,1 +cybium,1 +cyprus review,1 +cyta: journal of food,1 +cytogenetic and genome research,1 +cytokine,1 +cytokine and growth factor reviews,1 +cytologia,1 +cytometry part a,1 +cytometry part b: clinical cytometry,1 +cytopathology,1 +cytoskeleton,1 +cytotechnology,1 +cytotherapy,1 +czech journal of animal science,1 +czech journal of food sciences,1 +czech journal of genetics and plant breeding,1 +czechoslovak mathematical journal,1 +dacia: revue darcheologie et dhistoire ancienne,1 +dacoromania,1 +dados: revista de ciencias sociais,1 +daedalus,2 +daimon: revista de filosofia,1 +dairy industries international,1 +dairy science and technology,1 +dalhousie french studies,1 +dalhousie law journal,1 +dalhousie review,1 +dalton transactions,1 +dance chronicle,2 +dance research,2 +dance research journal,3 +danish medical journal,1 +danish yearbook of philosophy,1 +danish yearbook of musicology,1 +dansk sociologi,1 +dansk teologisk tidsskrift,1 +danske studier,1 +danske talesprog,1 +dante studies,1 +dao: a journal of comparative philosophy,1 +daol: discourse analysis online,1 +daphnis: zeitschrift für mittlere deutsche literatur und kultur der frühen neuzeit,1 +das argument: zeitschrift für philosophie und sozialwissenschaften,1 +das zeichen: zeitschrift fur sprache und kultur gehörloser,1 +data and knowledge engineering,2 +data base for advances in information systems,1 +data compression conference,1 +data mining and knowledge discovery,3 +data 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literatur,1 +deutsche entomologische zeitschrift,1 +deutsche lebensmittel-rundschau,1 +deutsche mathematiker vereinigung: jahresbericht,1 +deutsche medizinische wochenschrift,1 +deutsche orient-gesellschaft: mitteilungen,1 +deutsche sprache,2 +deutsche vierteljahrsschrift für literaturwissenschaft und geistesgeschichte,3 +deutsche zeitschrift für philosophie,1 +deutsche zeitschrift für sportmedizin,1 +deutsches archiv für erforschung des mittelalters,2 +deutsches ärzteblatt: ausgabe a: ärztliche mitteilungen,1 +deutsches arzteblatt international,1 +deutsches schiffartsarchiv,1 +developing economies,1 +developing world bioethics,1 +development,1 +development,2 +development and change,3 +development and psychopathology,2 +development genes and evolution,1 +development growth and differentiation,1 +development in practice,1 +development policy review,1 +development southern africa,1 +developmental and comparative immunology,1 +developmental biology,1 +developmental cell,3 +developmental 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social practice,1 +diacritics: a review of contemporary criticism,3 +diadora,1 +diagnostic and interventional radiology,1 +diagnostic and therapeutic endoscopy,1 +diagnostic cytopathology,1 +diagnostic microbiology and infectious disease,1 +diagnostic molecular pathology,1 +diagnostic pathology,1 +diagnostica,1 +diakonian tutkimus,1 +dialectica,2 +dialectical anthropology,2 +dialectologia et geolinguistica,1 +zeitschrift für kulturphilosophie,1 +dialog: a journal of theology,1 +dialogue: canadian philosophical review,1 +dialogues d'histoire ancienne,1 +dialogues in human geography,2 +dialysis and transplantation,1 +diamond and related materials,1 +diaspora: a journal of transnational studies,2 +"diasporas, histoire et sociétés",1 +diaspory: nezavisimyj nauchnyj zhurnal,1 +diatom research,1 +dichtung-digital,1 +dickens quarterly,1 +dickens studies annual,1 +dickensian,1 +dictionaries: journal of the dictionary society of north america,1 +dictionary of literary biography,1 +didaskalia: ancient theater today,1 +diderot studies,1 +die casting engineer,1 +die friedens-warte,1 +die laute: jahrbuch der deutschen lautengesellschaft,1 +die philosophin,1 +die verwaltung: zeitschrift für verwaltungsrecht und verwaltungswissenschaften,1 +diedut,1 +dielheimer blätter zum alten testament und seiner rezeption in der alten kirche,1 +diesel progress north american edition,1 +differences: a journal of feminist cultural studies,3 +differential and integral equations,1 +differential equations,1 +differential equations and applications,1 +differential equations and dynamical systems: an international journal for theory and applications,1 +differential geometry and its applications,1 +differential geometry: dynamical systems,1 +differentiation,1 +solid state phenomena,1 +defect and diffusion forum,1 +diffusion fundamentals,1 +digest journal of nanomaterials and biostructures,1 +ieee international solid-state circuits conference,2 +ieee radio frequency integrated circuits symposium digest of papers,1 +digestion,1 +digestive and liver disease,1 +digestive diseases,1 +digestive diseases and sciences,1 +digestive endoscopy,1 +digestive surgery,1 +digital creativity,2 +digital formations,1 +digital humanities quarterly,1 +nordic journal of digital literacy,1 +digital signal processing,1 +dike,1 +din : religionsvitenskapelig tidsskrift,1 +diogenes,1 +dionysius,1 +diplomacy and statecraft,1 +diplomatic history,2 +diplomatic studies,1 +diritto e giustizia,1 +diritto penale e processo,1 +diritto pubblico,1 +disability and society,2 +disability and health journal,1 +disability and rehabilitation,1 +disability and rehabilitation: assistive technology,1 +disability studies quarterly,1 +disaster advances,0 +disaster medicine and public health preparedness,1 +disaster prevention and management,1 +disasters,2 +discours social: analyse du discours et sociocritique des textes,1 +discourse: studies in the cultural politics of education,2 +discourse and communication,2 +discourse and society,2 +discourse: journal for theoretical studies in media and culture,1 +"discourse approaches to politics, society and culture",1 +discourse processes,2 +discourse studies,3 +discourses in dance,1 +discrete and computational geometry,2 +discrete and continuous dynamical systems: series a,1 +discrete and continuous dynamical systems: series b,1 +discrete applied mathematics,2 +discrete dynamics in nature and society,1 +discrete event dynamic systems: theory and applications,1 +discrete mathematics,1 +discrete mathematics and theoretical computer science,1 +discrete optimization,1 +discussiones mathematicae: probability and statistics,1 +disease markers,0 +disease models and mechanisms,2 +diseases of aquatic organisms,1 +diseases of the colon and rectum,1 +diseases of the esophagus,1 +diskus: the on-disk journal of international religious studies,1 +diskussion musikpaedagogik,1 +dislocations in solids,1 +disp,1 +displays,1 +disputatio,1 +dissent,1 +dissertationes mathematicae,1 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environmental law and policy forum,1 +duke journal of comparative and international law,1 +duke journal of gender law and policy,1 +duke law journal,2 +duke mathematical journal,3 +dumbarton oaks papers,2 +duodecim,1 +durability and damage tolerance of composite materials and structures,1 +dutch crossing: a journal of low countries studies,1 +dutch journal for music theory,1 +dve domovini-two homelands,1 +dvt: dejiny ved a techniky,1 +dyes and pigments,1 +dynamic systems and applications,0 +dynamical systems: an international journal,1 +dynamics of atmospheres and oceans,1 +"dynamics of continuous, discrete and impulsive systems series a: mathematical analysis",1 +dynamics of partial differential equations,1 +dynamis,1 +dyslexia,2 +dysphagia,2 +dzieje najnowsze,1 +eandmj: engineering and mining journal,1 +ear and hearing,3 +early american literature,2 +early american studies: an interdisciplinary journal,1 +early child development and care,1 +early childhood education journal,1 +early childhood research and practice,1 +early childhood research quarterly,2 +early china,1 +early christianity,2 +early education and development,1 +early human development,1 +early intervention in psychiatry,1 +early keyboard journal,1 +early medieval europe,3 +early modern and modern studies,1 +early modern literary studies,1 +early modern women: an interdisciplinary journal,1 +early music,2 +early music history,3 +early popular visual culture,1 +early science and medicine,1 +early theatre,1 +early years: an international research journal,1 +earth and environmental science transactions of the royal society of edinburgh,1 +earth and planetary science letters,3 +earth interactions,1 +earth moon and planets,1 +earth planets and space,1 +earth sciences history,1 +earth sciences research journal,1 +earth surface processes and landforms,2 +earth system dynamics,1 +earthquake engineering and structural dynamics,2 +earthquake engineering and engineering vibration,1 +earthquake science,1 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policy,1 +genos,1 +genre,1 +geojournal,1 +geoacta,1 +geoarabia,1 +geoarchaeology: an international journal,2 +geobiology,2 +geobios,1 +geochemical journal,1 +geochemical transactions,1 +geochemistry geophysics geosystems,2 +geochemistry international,1 +geochemistry: exploration environment analysis,1 +geochimica et cosmochimica acta,2 +geochronometria,1 +geoderma,2 +geodetski list,1 +geodetski vestnik,1 +geodesy and cartography,1 +geodiversitas,1 +geofisica internacional,1 +geofizika,1 +geofluids,1 +geoforum,3 +geografie,1 +geografisk tidsskrift: danish journal of geography,1 +geografiska annaler series a: physical geography,1 +geografiska annaler series b: human geography,2 +geografiska notiser,1 +geographia antiqua,1 +geographical analysis,2 +geographical journal,1 +geographical research,1 +geographical review,1 +geographie economie societe,1 +geographie physique et quaternaire,1 +geographische zeitschrift,1 +geography,1 +geography compass,2 +geoheritage,1 +geoinformatica,1 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monatsschrift,3 +germanistik : deutsche sprach- und literaturwissenschaft,1 +germanistik : internationales referatenorgan mit bibliographischen hinweisen,1 +germanistische linguistik,1 +germanistische mitteilungen,1 +germanoslavica,1 +gerodontology,1 +gerontologia,1 +gerontologist,3 +gerontology,1 +geschichte der pharmazie,1 +geschichte in wissenschaft und unterricht,1 +geschichte lernen,1 +geschichte und gegenwart,1 +geschichte und gesellschaft,3 +gesprächsforschung,2 +gesta: international center of medieval art,2 +gestalt review,1 +gestion y politica publica,1 +gesture,2 +gesture studies,1 +gesunde pflanzen,1 +gesundheitsokonomie und qualitatsmanagement,1 +gesundheitswesen,1 +gewerblicher rechtsschutz und urheberrecht,1 +studium: tijdschrift voor wetenschaps- en universiteitsgeschiedenis,1 +gezelliana,1 +gff,1 +gi cancer,1 +gifted child quarterly,2 +gim international,1 +gineco ro,1 +ginecologia y obstetricia clinica,1 +ginekologia polska,1 +giornale critico della filosofia italiana,1 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journal of pure and applied mathematics,1 +global jurist,1 +global media and communication,1 +global media journal,0 +global nest journal,1 +global networks: a journal of transnational affairs,2 +global public health,1 +global social policy,1 +global society,1 +global telecoms business,1 +"globalisation, societies and education",1 +globalizations,2 +glossa,1 +glossos,1 +glot international,1 +glotta: zeitschrift fur griechische und lateinische sprache,2 +glq: a journal of lesbian and gay studies,2 +glycobiology,1 +glycoconjugate journal,1 +gms health technology assessment,1 +gms medizin-bibliothek-information,1 +gnomon: kritische zeitschrift fur die gesamte klassische altertumswissenschaft,2 +goethe jahrbuch,1 +goethe yearbook,1 +gold bulletin,1 +gondwana research,3 +gospodarka surowcami mineralnymi-mineral resources management,1 +gosudarstvennoe i munitsipal´noe upravlenija,1 +gosudarstvo i pravo,1 +goteborg studies in conservation,1 +gothenburg papers in theoretical linguistics,1 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journal,1 +law quarterly review,2 +law text culture,1 +"law, culture and the humanities",1 +"law, environment and development journal",1 +"law, probability and risk: a journal of reasoning under uncertainty",1 +"law, social justice and global development",1 +laval theologique et philosophique,1 +"marburger beiträge zur antiken handels-, wirtschafts- und sozialgeschichte",1 +lc gc europe,0 +lc gc north america,0 +le droit maritime francais,1 +leadership,1 +leadership and management in engineering,1 +leadership and organization development journal,1 +leadership and policy in schools,1 +leadership in health services,1 +leadership quarterly,3 +learned publishing,1 +learning and behavior,1 +learning and memory,2 +learning and individual differences,3 +learning and instruction,3 +learning and motivation,1 +learning and teaching in higher education,1 +learning and teaching: the international journal of higher education in the social sciences,1 +learning disabilities research and practice,2 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szakfolyóirat,1 +lendemains: etudes comparees sur la france,1 +lengas: revue sociolinguistique,1 +lenguas modernas,1 +lenseignement mathematique,1 +leonardo,3 +leonardo electronic almanac,1 +digest of the leos summer topical meetings,1 +leprosy review,1 +ler historia,1 +les cahiers du rifal,1 +les houches,1 +leshonenu,1 +lessing yearbook,1 +lethaia,1 +letras cubanas,1 +letras femeninas,1 +letteratura italiana antica,1 +letterature d america,1 +lettere italiane,2 +letters in applied microbiology,1 +letters in drug design and discovery,1 +letters in mathematical physics,1 +letters in organic chemistry,1 +leukemia,3 +leukemia & lymphoma,1 +leukemia research,1 +leukos,1 +leuvense bijdragen: tijdschrift voor germaanse filologie,1 +levant,2 +leviathan: zeitschrift fur sozialwissenschaft,1 +lex localis: journal of local self: government,1 +lexicographica: internationales jahrbuch fur lexikographie,1 +lexicographica: series maior: supplementbände zum internationalen jahrbuch für lexikographie,1 +lexicometrica,1 +lexiconordica,1 +lexikos,0 +lexique,1 +lexis,1 +lexis: revista de linguistica y literatura,1 +lhistoire,1 +lianes,1 +lias: journal of early modern intellectual culture and its sources,1 +libertarian papers,1 +liberte,1 +information and culture,1 +library,1 +library and information science research,3 +library and archival security,1 +library and information research,1 +library and information science,1 +library hi tech,1 +library journal,1 +library management,1 +library philosophy and practice,1 +library quarterly,1 +library resources and technical services,1 +library trends,1 +libres,1 +libri,1 +libya antiqua: annual of the department of antiuities of libya,1 +libyan studies,1 +the lichenologist,1 +lidil,1 +lied und populare kultur-song and popular culture,1 +lietuvos archaeologija,1 +lietuvos etnologija: socialines antropologija i etnologija studijos,1 +life science journal: acta zhengzhou university overseas edition,1 +life sciences,1 +lifetime data analysis,1 +ligeia: dossiers sur lart,1 +light and engineering,1 +lighting research and technology,2 +liikunta ja tiede,1 +lilith: a feminist history journal,1 +zeitschrift für literaturwissenschaft und linguistik,2 +limba romana,1 +limnetica,1 +limnologica,1 +limnology,1 +limnology and oceanography,3 +limnology and oceanography: methods,1 +lindbergia,1 +linear and multilinear algebra,1 +linear algebra and its applications,2 +linformation litteraire,1 +lingua,1 +lingua e stile,1 +lingua et linguistica,1 +lingua nostra,1 +linguistic analysis,1 +linguistic approaches to literature,1 +linguistic association of korea journal,1 +linguistic discovery,1 +linguistic inquiry,3 +linguistic insights: studies in language and communication,1 +linguistic review,3 +linguistic typology,3 +linguistic variation,1 +linguistica biblica,1 +linguistica espanola actual,1 +linguistica lettica,1 +linguistica palatina,1 +linguistica pragensia,1 +linguistica silesiana,1 +linguistica uralica,1 +linguistica y literatura,1 +linguistics,3 +linguistics and education,2 +linguistics and philology,1 +linguistics and philosophy,3 +linguistics and the human sciences,1 +linguistics in the netherlands,1 +linguistics of the tibeto-burman area,1 +linguistik aktuell,1 +linguistik online,1 +linguistique,1 +linguistische arbeiten,2 +linguistische berichte,1 +lingvisticae investigationes,1 +lingvisticae investigationes supplementa,1 +linquistique africaine,1 +linux journal,0 +linx,1 +lion and the unicorn,1 +lipids,2 +lipids in health and disease,1 +liquid crystals,1 +higher-order and symbolic computation,1 +listy cukrovarnicke a reparske,1 +literacy,1 +literary and linguistic computing,2 +literary research,1 +literatur fur leser,1 +literatur und kritik,1 +literatura,1 +literatura mexicana,1 +literatura y linguistica,1 +literature and history: third series,2 +literature and aesthetics,1 +literature and medicine,2 +literature and theology,3 +literature-film quarterly,1 +lithic technology,1 +lithics,1 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analyse,1 +logopedics phoniatrics vocology,1 +logos,1 +logos and pneuma: chinese journal of theology,1 +logos: anales del seminario de metafisica,1 +logos: a journal of catholic thought and culture,1 +logos: vilnius,1 +loisir et societe,1 +london journal,1 +london mathematical society lecture notes,1 +london oriental and african language library,1 +london review of education,1 +long range planning,3 +journal of social work in end-of-life and palliative care,1 +louvain studies,1 +lov og rett: norsk juridisk tidsskrift,1 +low temperature physics,1 +lsp journal,1 +lubrication science,1 +lucentum,1 +lud,1 +ludus: medieval and early renaissance theatre and drama,1 +luminescence,1 +lund archaeological review,1 +lung,1 +lung cancer,1 +lunula: archaeologia protohistorica,1 +lupus,1 +luso: brazilian review,2 +lustrum,1 +luther,1 +lutherjahrbuch,2 +lwt: food science and technology,1 +lychnos: lardomshistoriska samfundets arsbok = annual of the swedish history of science society,1 +lykia,1 +lymphatic research and biology,1 +lymphology,1 +lähivõrdlusi-lähivertailuja,1 +médecine sciences,1 +manufacturing and service operations management,3 +m/c journal,1 +m@n@gement,1 +maal og minne,1 +maanmittaus,1 +maarav: a journal for the study of the northwest semitic languages and literatures,1 +maastricht journal of european and comparative law,3 +macedonian journal of chemistry and chemical engineering,0 +machine learning,3 +machine vision and applications,2 +machining science and technology,1 +macroeconomic dynamics,1 +macromolecular bioscience,1 +macromolecular chemistry and physics,1 +macromolecular materials and engineering,1 +macromolecular rapid communications,1 +macromolecular reaction engineering,1 +macromolecular research,1 +macromolecular symposia,1 +macromolecular theory and simulations,1 +macromolecules,3 +madera y bosques,1 +maderas: ciencia y tecnologia,1 +madoc: tijdschrift over de middel eeuwen,1 +magallania,1 +magazine of concrete research,1 +maghreb-machrek,1 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biotechnology,1 +marine chemistry,1 +marine drugs,1 +marine ecology: an evolutionary perspective,1 +marine ecology: progress series,2 +marine environmental research,1 +marine genomics,1 +marine geodesy,1 +marine geology,2 +marine geophysical researches,1 +marine georesources and geotechnology,1 +marine mammal science,1 +marine micropaleontology,1 +marine ornithology,1 +marine policy,2 +marine pollution bulletin,1 +marine resource economics,1 +marine structures,3 +(mt) marine technology,1 +marine technology society journal,1 +mariners mirror,1 +maritime economics and logistics,1 +maritime policy and management,1 +newsletter - australian centre for maritime studies,1 +marius,1 +marketing health services,1 +marketing intelligence and planning,1 +marketing letters,1 +marketing science,3 +marketing theory,2 +markov processes and related fields,1 +marriage and family review,1 +marvels and tales: journal of fairy-tale studies,1 +maske und kothurn,1 +mass communication and society,1 +mass spectrometry reviews,1 +massachusetts review,1 +matatu,1 +match: communications in mathematical and in computer chemistry,1 +matematicki vesnik,1 +material culture review,1 +material religion,2 +materiale plastice,1 +materiales de construccion,1 +materiali e contributi per la storia della narrativa greco-latina,1 +materiali e discussioni per lanalisi dei testi classici,2 +materiali in tehnologije,1 +"materialisten: tidsskrift for forskning, fagkritikk og teoretisk debatt",1 +materials & design,3 +materials and corrosion-werkstoffe und korrosion,1 +materials and manufacturing processes,1 +materials and structures,1 +materials at high temperatures,1 +materials characterization,1 +materials chemistry and physics,1 +materials evaluation,1 +materials letters,1 +materials performance,1 +materials physics and mechanics,1 +materials research bulletin,1 +materials research innovations,1 +materials research society symposia proceedings,1 +materials research: ibero-american journal of materials,1 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programming,3 +mathematical reports of the academy of science,1 +mathematical research letters,2 +mathematical social sciences,1 +mathematical structures in computer science,1 +mathematical thinking and learning,2 +mathematics and computer education,1 +mathematics and computers in simulation,1 +mathematics and financial economics,1 +mathematics and mechanics of solids,1 +mathematics education research journal,1 +mathematics education review,1 +mathematics in computer science,1 +mathematics of computation,3 +mathematics of control signals and systems,1 +mathematics of operations research,3 +mathematik lehren,1 +mathematika,1 +mathematische annalen,3 +mathematische nachrichten,1 +mathematische semesterberichte,1 +mathematische zeitschrift,2 +matkailututkimus,1 +matrix biology,2 +maturitas,1 +mausam,1 +max planck commentaries on world trade law,1 +max planck yearbook of united nations law,1 +mayo clinic proceedings,2 +molecular and cellular biomechanics,1 +mcgill law journal,1 +mcn: the american journal of maternal-child nursing,1 +meander,1 +measurement,2 +measurement and control,1 +measurement and evaluation in counseling and development,1 +measurement in physical education and exercise science,1 +measurement science and technology,2 +measurement science review,1 +measurement techniques,1 +measurement: interdisciplinary research and perspectives,1 +measuring business excellence,1 +meat science,2 +mechanics & industry,1 +meccanica,1 +mechanical engineering,1 +mechanical systems and signal processing,3 +mechanics based design of structures and machines,1 +mechanics of advanced materials and structures,1 +mechanics of composite materials,1 +mechanics of materials,2 +mechanics of time-dependent materials,1 +mechanics research communications,1 +mechanika,1 +mechanism and machine theory,2 +mechanisms of ageing and development,1 +mechatronics,2 +meddelelser fra ny carlsberg glyptotek,1 +"meddelelser om groenland, man and society",1 +meddelelser om konservering,1 +medecine et chirurgie du pied,1 +medecine et droit,1 +medecine therapeutique pediatrie,1 +mededelingen van het cyriel buysse genootschap,1 +mededelingen vanwege het spinozahuis,1 +media ja viestintä,2 +media culture and society,3 +media development,1 +media history,2 +media history monographs,1 +media international australia,1 +media psychology,2 +"media, war and conflict",1 +mediaevalia,1 +mediaevalia historica bohemica,1 +mediaevalia: textos e estudos,1 +mediaevistik: internationale zeitschrift fur interdisziplinare mittelalterforschung,1 +mediations,1 +mediators of inflammation,1 +medical and biological engineering and computing,1 +medical and veterinary entomology,1 +medical anthropology,3 +medical anthropology quarterly,2 +medical care,2 +medical care research and review,1 +medical clinics of north america,2 +medical decision making,3 +medical dosimetry,1 +medical education,3 +medical education online: an electronic journal,1 +medical engineering and physics,1 +medical history,2 +medical humanities,1 +medical hypotheses,1 +medical image analysis,3 +medical journal of australia,1 +medical laser application,1 +medical law review,2 +medical letter on drugs and therapeutics,1 +medical microbiology and immunology,1 +medical molecular morphology,1 +medical mycology,1 +medical oncology,1 +medical physics,1 +medical principles and practice,1 +medical problems of performing artists,1 +medical science monitor,1 +medical teacher,1 +medicc review,1 +medicina clinica,1 +medicina del lavoro,1 +medicina dello sport,1 +medicina intensiva,1 +medicina nei secoli,1 +medicina oral patologia oral y cirugia bucal,1 +medicina veterinaria: recife,1 +medicina: buenos aires,1 +medicinal chemistry,1 +medicinal chemistry research,1 +medicinal research reviews,2 +medicina,1 +medicine,1 +medicine and science in sports and exercise,3 +medicine health care and philosophy,1 +medicine science and the law,1 +"medicine, conflict, and survival",1 +medicinski glasnik,1 +mediekultur,1 +medien und kommunikationswissenschaft,1 +medien journal,1 +medieval and early modern science,1 +medieval and renaissance drama in england,1 +medieval archaeology,2 +medieval ceramics: journal of the medieval pottery research group,0 +medieval clothing and textiles,1 +medieval encounters,1 +medieval english theatre,1 +medieval feminist forum,1 +medieval history journal,1 +medieval perspectives,1 +medieval philosophy and theology,1 +medieval prosopography: history and collective biography,1 +medieval scandinavia,1 +medieval studies,1 +medievales,1 +medievalia et humanistica,2 +medievalismo,1 +medioevo,1 +medioevo e rinascimento,1 +medioevo greco,1 +medioevo romanzo,1 +mediterranean archaeology,1 +mediterranean historical review,2 +mediterranean journal of mathematics,1 +mediterranean language review,1 +mediterranean marine science,1 +mediterranean politics,1 +mediterranean quarterly,1 +mediterranean studies,1 +mediterranea: ricerche storiche,1 +"mediterraneo antico: economie, societa, culture",1 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process metallurgy and materials processing science,2 +metallurgist,1 +metals and materials international,1 +metalurgia international,1 +metalurgija,1 +metamaterials,1 +metaphilosophy,2 +metaphor and symbol,3 +metaphorik.de,1 +metaphysica,1 +metascience,1 +meteoritics and planetary science,1 +meteorological applications,1 +meteorologische zeitschrift,1 +meteorology and atmospheric physics,1 +method and theory in the study of religion,3 +methodology and computing in applied probability,1 +methodology: european journal of research methods for the behavioral and social sciences,1 +methods,1 +methods and applications of analysis,1 +methods and findings in experimental and clinical pharmacology,1 +methods in cell biology,1 +methods in enzymology,1 +methods in microbiology,1 +methods of biochemical analysis,1 +methods of information in medicine,3 +metis,1 +metrika,1 +metroeconomica: international review of economics,1 +metrologia,2 +metron,1 +metsätieteen aikakauskirja,1 +metu journal of the faculty of architecture,1 +mexican studies-estudios mexicanos,1 +mfs: modern fiction studies,3 +michigan journal of gender and law,1 +michigan journal of international law,2 +michigan law review,2 +michigan mathematical journal,1 +michigan quarterly review,1 +micro and nano letters,1 +microbes and environments,1 +microbes and infection,1 +microbial biotechnology,1 +microbial cell factories,1 +microbial drug resistance,1 +microbial ecology,2 +microbial pathogenesis,1 +microbiological research,1 +microbiology,1 +microbiology and immunology,1 +microbiology and molecular biology reviews,2 +microbiology-sgm,1 +microchemical journal,1 +microchimica acta,1 +microcirculation,1 +microelectronic engineering,1 +microelectronics international,1 +microelectronics journal,1 +microelectronics reliability,1 +microfluidics and nanofluidics,1 +microgravity science and technology,1 +micron,1 +micropaleontology,1 +microporous and mesoporous materials,2 +microprocessors and microsystems,1 +microscopy and microanalysis,1 +microscopy research and technique,1 +microsurgery,1 +microsystem technologies: micro-and nanosystems-information storage and processing systems,1 +microvascular research,1 +microwave and optical technology letters,1 +microwave journal,1 +middle east journal,2 +middle east journal of culture and communication,1 +middle east policy,1 +middle east quarterly,1 +middle east report,1 +middle eastern literatures,1 +middle eastern studies,1 +midland history,2 +midwest quarterly: a journal of contemporary thought,1 +midwest studies in philosophy,2 +conference proceedings : midwest symposium on circuits and systems,1 +midwifery,2 +migration: a european journal of international migration and ethnic relation,1 +mikologiya i fitopatologiya,1 +milan journal of mathematics,1 +milbank quarterly,3 +militargeschichtliche zeitschrift,1 +military balance,1 +military law review,1 +military medicine,1 +military operations research,1 +military psychology,1 +militärhistorisk tidskrift,1 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medicinal chemistry,1 +mini: reviews in organic chemistry,1 +minnesota law review,1 +minnesota review,1 +minnesota symposia on child psychology,1 +minos,1 +minzu yuwen,1 +mir i politika,1 +mir rossii,2 +mir russkogo slova,1 +mirator,1 +mirovaâ èkonomika i meždunarodnye otnošeniâ,1 +mis quarterly,3 +mis quarterly executive,2 +miscelanea: a journal of english and american studies,1 +miscellanea francescana: rivista trimestrale di scienze teologiche e di studi francescani,1 +miskolc mathematical notes,1 +missiology: an international review,1 +mission studies,2 +missionalia,1 +mississippi quarterly,1 +mit electronic journal for middle east studies,1 +mit sloan management review,2 +mitigation and adaptation strategies for global change,1 +mitkufat haeven: journal of the israel prehistoric society,1 +mitochondrial dna,1 +mitochondrion,1 +zitteliana reihe a: mitteilungen der bayerischen staatssammlung fur palaontologie und geologie,1 +"mitteilungen der berliner gesellschaft fur anthropologie, ethnologie und urgeschichte",1 +mitteilungen der osterreichischen geographischen gesellschaft,1 +mitteilungen des deutschen archaologischen instituts: abteilung kairo,1 +mitteilungen des deutschen archaologischen instituts : athenische abteilung,2 +mitteilungen des deutschen archaologischen instituts: romische abteilung,2 +istanbuler mitteilungen,1 +mitteilungen des deutschen archaologischen instituts: abteilung madrid,1 +mitteilungen des instituts fur osterreichische geschichtsforschung,1 +mitteilungen des kunsthistorischen institutes in florenz,2 +mitteilungen klosterneuburg,1 +mitteilungen zur christlichen archaologie,1 +mittellateinische studien und texte,2 +mittellateinisches jahrbuch,1 +mla news,1 +mljekarstvo,1 +mln,2 +mnimon,1 +mnemosyne,2 +"mnemosyne, supplements",2 +journal of mobile information systems,0 +mobile networks and applications,1 +mobilities,2 +mobilization,2 +model assisted statistics and applications,1 +modeles linguistiques,1 +modeling identification and control,1 +modelling and simulation in materials science and engineering,1 +modern and contemporary france,2 +modern asian studies,2 +modern china,2 +modern drama,2 +modern english teacher,1 +modern greek studies,1 +modern intellectual history,2 +modern italy,1 +modern judaism,1 +modern language journal,3 +modern language quarterly,3 +modern language review,1 +modern language studies,1 +modern law science,1 +modern pathology,2 +modern philology,2 +modern physics letters a,1 +modern physics letters b,1 +modern rheumatology,1 +modern theology,3 +moderna språk,1 +moderne sprachen,1 +modernism-modernity,2 +moenia: revista lucense de lingustica and literatura,1 +mokuzai gakkaishi,1 +molecular and cellular proteomics,2 +molecular and cellular toxicology,1 +molecular and biochemical parasitology,1 +molecular and cellular biochemistry,1 +molecular and cellular biology,2 +molecular and cellular endocrinology,1 +molecular and cellular neuroscience,1 +molecular and cellular probes,1 +molecular 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western history,0 +monte carlo methods and applications,1 +monthly labor review,1 +monthly notices of the royal astronomical society,2 +monthly notices of the royal astronomical society: letters,3 +monthly review: an independent socialist magazine,1 +monthly weather review,1 +monti: monographs in translation and interpretation,1 +monumenta graeca et romana,1 +monumenta nipponica,2 +monumenta serica,1 +monumental,1 +monuments et mémoires de la fondation eugene piot,1 +moreana,1 +morphology,2 +mortality,1 +mosaic: a journal for the interdisciplinary study of literature,3 +moscow mathematical journal,1 +motivation and emotion,1 +motor control,1 +motricite cerebrale: readaptation neurologie du developpement,1 +motriz: revista de educacao fisica,1 +mots: les langages du politique,1 +mountain research and development,1 +mouseion,1 +moussons,1 +mouvement social,2 +movement disorders,3 +movimento,1 +moyen age,1 +moyen francais,1 +mrs bulletin,2 +mrs internet journal of nitride semiconductor research,1 +mucosal immunology,1 +muinaistutkija,1 +muinasaja teadus,1 +multibody system dynamics,2 +multicultural perspectives,1 +multidimensional systems and signal processing,1 +multidisciplinary respiratory medicine,1 +multilingua: journal of cross-cultural and interlanguage communication,2 +multimedia systems,1 +multimedia tools and applications,1 +multinational finance journal,1 +multiphase science and technology,1 +multiple sclerosis,2 +multiscale modeling and simulation,1 +multitudes,1 +multivariate behavioral research,1 +munchener jahrbuch der bildenden kunst,1 +munchener studien zur sprachwissenschaft,1 +munchener theologische zeitschrift,1 +munster: zeitschrift fur christliche kunst und kunstwissenschaft,1 +muqarnas,1 +muscle and nerve,1 +musculoskeletal care,1 +museologia scientifica: rivista dell a.n.m.s.,1 +museon,1 +museum and society,2 +museum anthropology,1 +museum anthropology review,1 +museum helveticum,2 +museum international,2 +museum management and curatorship,2 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reviews in mutation research,1 +muttersprache,1 +mùzeum,1 +muzikoloski zbornik,1 +muzyka: kwartalnik poswiecony historii i teorii muzyki,1 +mycologia,2 +mycological progress,1 +mycological research,1 +mycopathologia,1 +mycorrhiza,1 +mycoscience,1 +mycoses,1 +mycotaxon,1 +mycotoxin research,1 +myrtia: revista de filologia clasica,1 +n a b u: nouvelles assyriologiques breves et utilitaires,1 +n:paradoxa: international feminist art journal,1 +naamkunde,1 +nachrichten aus der chemie,0 +nacta journal,1 +nagoya mathematical journal,1 +namenkundliche informationen,1 +names,2 +nammco scientific publications,1 +namn och bygd,1 +namn og nemne: tidsskrift for norsk namnegransking,1 +"nan nu: men, women and gender in early and imperial china",1 +nano,1 +nano letters,3 +nano research,2 +nano today,3 +nanomedicine,1 +nanomedicine: nanotechnology biology and medicine,2 +nanoscale,3 +nanoscale and microscale thermophysical engineering,1 +nanotechnology,2 +nanotoxicology,2 +napis: tom poswiecony literaturze okolicznosciowej i uzytkowej,1 +narodna umjetnost,1 +narrative,2 +narrative inquiry,2 +nasarre: revista aragonesa de musicologia,1 +nase rec,1 +nashim: a journal of jewish womens studies,1 +nassauische annalen,1 +nathaniel hawthorne review,1 +nation,1 +proceedings of the aaai conference on artificial intelligence,2 +national gallery technical bulletin,1 +national identities,2 +national institute economic review,1 +national medical journal of india,1 +national tax journal,1 +nationalism and ethnic politics,1 +nationalities papers,1 +nationalmuseets arbejdsmark,1 +nations and nationalism,3 +"nato science series: sub series i, life and behavioural sciences",1 +natur und recht,1 +natural areas journal,1 +natural computing,1 +natural hazards,1 +natural hazards and earth system sciences,1 +natural hazards review,1 +natural history,1 +natural language and linguistic theory,3 +natural language engineering,3 +natural language semantics,2 +natural product communications,1 +natural product reports,1 +natural product research,1 +natural resource modeling,1 +natural resources forum,1 +natural resources journal,1 +natural resources research,1 +nature,3 +nature and resources,1 +nature biotechnology,3 +nature cell biology,3 +nature chemical biology,3 +nature chemistry,3 +nature climate change,3 +nature communications,3 +nature genetics,3 +nature geoscience,3 +nature immunology,3 +nature materials,3 +nature medicine,3 +nature methods,3 +nature nanotechnology,3 +nature neuroscience,3 +nature photonics,3 +nature physics,3 +nature protocols,1 +nature reviews cancer,2 +nature reviews cardiology,2 +nature reviews clinical oncology,2 +nature reviews drug discovery,3 +nature reviews endocrinology,2 +nature reviews gastroenterology and hepatology,2 +nature reviews genetics,2 +nature reviews immunology,3 +nature reviews microbiology,3 +nature reviews molecular cell biology,2 +nature reviews nephrology,2 +nature reviews neurology,3 +nature reviews neuroscience,3 +nature reviews rheumatology,2 +nature reviews urology,2 +nature structural and molecular biology,3 +natures sciences societes,1 +natureza and conservacao,1 +the science of nature,1 +sociologiâ vlasti,1 +naunyn-schmiedebergs archives of pharmacology,1 +nautilus,1 +naval engineers journal,1 +naval research logistics,1 +navigation,2 +nordic and baltic journal of information and communications technologies,1 +nber macroeconomics annual,1 +ndt & e international,2 +near eastern archaeology,1 +near surface geophysics,1 +nebraska symposium on motivation,1 +nederlands kunsthistorisch jaarboek,1 +nederlands theologisch tijdschrift,1 +nederlands tijdschrift voor geneeskunde,1 +nederlandse letterkunde,1 +nederlandse taalkunde,1 +internationale neerlandstiek,1 +neerlandistiek.nl,1 +nefrologia,1 +neftyanoe khozyaistvo - oil industry,1 +negotiation journal,1 +nelinijni kolivannâ,1 +nematology,1 +neohelicon,2 +neonatology,2 +neophilologus,2 +neoplasia,2 +neoplasma,1 +neotestamentica,2 +neotropical entomology,1 +neotropical ichthyology,1 +nephrologie et therapeutique,1 +nephrology,1 +nephrology dialysis transplantation,2 +nephrology nursing journal,1 +neprajzi ertesito,1 +nervenarzt,1 +nervenheilkunde,1 +netherlands international law review,1 +netherlands journal of geosciences-geologie en mijnbouw,1 +netherlands journal of medicine,0 +netherlands quarterly of human rights,2 +netherlands yearbook of international law,1 +netnomics: economic research and electronic networking,1 +network: computation in neural systems,1 +networker: association for computing machinery,1 +networks,2 +networks and spatial economics,1 +networks and heterogeneous media,1 +neue politische literatur,1 +"neue praxis: zeitschrift für sozialarbeit, sozialpädagogik und sozialpolitik",1 +neue romania,1 +neue rundschau,1 +neue zeitschrift fur systematische theologie und religionsphilosophie,3 +neues jahrbuch fur geologie und palaontologie: abhandlungen,1 +neues jahrbuch fur mineralogie: abhandlungen,1 +neural computation,3 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neurophysiology and neuroscience",1 +neurology psychiatry and brain research,1 +neuromodulation,1 +neuromolecular medicine,1 +neuromuscular disorders,1 +neuron,3 +neuron glia biology,1 +neuro-oncology,2 +neuro-ophthalmology,1 +neuropathology,1 +neuropathology and applied neurobiology,1 +neuropediatrics,1 +neuropeptides,1 +neuropharmacology,3 +neurophysiologie clinique-clinical neurophysiology,1 +neurophysiology,1 +neuropsychiatric disease and treatment,1 +neuropsychobiology,1 +neuropsychologia,2 +neuropsychological rehabilitation,1 +neuropsychology,2 +neuropsychology review,2 +neuropsychopharmacology,3 +neuroquantology,1 +neuroradiology,1 +neurorehabilitation,1 +neurorehabilitation and neural repair,2 +neuroreport,1 +neuroscience,2 +neuroscience and behavioral physiology,1 +neuroscience and biobehavioral reviews,3 +neuroscience letters,1 +neuroscience research,1 +neuroscience research communications,1 +neuroscientist,1 +neurosignals,1 +neurosurgery,2 +neurosurgery clinics of north america,1 +neurosurgery quarterly,1 +neurosurgical review,1 +neurotherapeutics,1 +neurotoxicity research,1 +neurotoxicology,1 +neurotoxicology and teratology,1 +neurourology and urodynamics,1 +neusis: the greek journal for the history and philosophy of science and technology,1 +new astronomy,1 +new astronomy reviews,1 +new balkan politics,1 +new biotechnology,1 +new carbon materials,1 +new cinemas: journal of contemporary film,1 +new concepts in polymer science,1 +new criminal law review,1 +new directions for adult and continuing education,1 +new directions for child and adolescent development,1 +new directions for evaluation,1 +new directions for higher education,1 +new directions for institutional research,1 +new directions for teaching and learning,1 +new directions for youth development,1 +new educational review,1 +new electronics,1 +new england journal of entrepreneurship,1 +the new england journal of medicine,3 +new england quarterly: a historical review of new england life and letters,1 +new england review: middlebury series,1 +new england theatre journal,1 +new forests,1 +new formations: a journal of culture/theory/politics,1 +new generation computing,1 +new genetics and society,1 +new german critique,3 +new german review,1 +new hibernia review,1 +new history,1 +new horizons in adult education and human resource development,1 +new ideas in psychology,1 +new journal of chemistry,1 +new journal of physics,2 +new left review,2 +new library world,1 +new literary history,3 +new mathematics and natural computation,1 +new media and society,3 +new medit,1 +guidebook of the new mexico geological society,1 +new mexico historical review,1 +new microbiologica,1 +new orleans review,1 +new perspectives quarterly,1 +new phytologist,3 +new political economy,3 +new political science: a journal of politics and culture,1 +new republic,1 +new review of academic librarianship,1 +new review of hypermedia and multimedia,1 +new review of information networking,1 +new solutions: a journal of environmental and occupational health policy: ns:,1 +new south wales public health bulletin,1 +new technology work and employment,1 +new testament studies,3 +"new testament tools, studies and documents",1 +new theatre quarterly,2 +new voices in classical reception studies,1 +new voices in translation studies,1 +new writing: the international journal for the practice and theory of creative writing,1 +new yearbook for phenomenology and phenomenological philosophy,2 +new york journal of mathematics,1 +new york review of books,0 +new york times book review,0 +new york university journal of international law and politics,1 +new york university law review,2 +new zealand geographer,1 +new zealand journal of agricultural research,1 +journal of pacific archaeology,1 +new zealand journal of botany,1 +new zealand journal of crop and horticultural science,1 +new zealand journal of ecology,1 +new zealand journal of educational studies,1 +new zealand journal of environmental law,1 +new zealand journal of geology and geophysics,1 +new zealand journal of history,1 +new zealand journal of marine and freshwater research,1 +new zealand journal of mathematics,1 +new zealand journal of psychology,1 +new zealand journal of zoology,1 +new zealand law review,1 +new zealand population review,1 +new zealand universities law review,1 +new zealand veterinary journal,1 +newborn and infant nursing review,1 +newsletters on stratigraphy,1 +newspaper research journal,1 +nevtani ertesito,1 +nexus network journal,1 +information: wissenschaft und praxis,1 +nhri symposium,1 +nicotine and tobacco research,1 +nieren- und hochdruckkrankheiten,1 +nietzsche-studien,1 +nihon reoroji gakkaishi,1 +niin & näin,1 +nijhoff law specials,1 +nikephoros: zeitschrift fur sport und kultur im altertum,1 +nineteenth century art worldwide,1 +nineteenth century gender studies,1 +nineteenth century music,2 +nineteenth century prose,2 +nineteenth century theatre and film,1 +nineteenth-century contexts,1 +nineteenth-century french studies,2 +nineteenth-century literature,3 +nineteenth-century music review,1 +nineteenth-century studies,1 +journal of the ceramic society of japan,1 +nippon suisan gakkaishi,1 +nir : nordiskt immateriellt rättsskydd,2 +nispacee journal of public administration and policy,1 +nitric oxide-biology and chemistry,1 +nj drama australia journal,1 +njas: wageningen journal of life sciences,1 +nmediac: the journal of new media and culture,1 +nmr in biomedicine,1 +noa: norsk som andrespråk,1 +nodea: nonlinear differential equations and applications,1 +noise and health,1 +nomadic peoples,1 +nomina,1 +nomina africana,1 +nondestructive testing and evaluation,1 +nonlinear analysis: modelling and control,1 +nonlinear analysis: real world applications,1 +nonlinear analysis: theory methods and applications,1 +nonlinear dynamics,2 +nonlinear dynamics and systems theory,1 +"nonlinear dynamics, psychology, and life sciences",1 +nonlinear phenomena in complex systems,1 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life studies,1 +nordic notes,1 +nordic psychology,1 +nordic pulp and paper research journal,1 +nordic social work research,1 +nordic studies in education,1 +nordic theatre studies,2 +nordica,1 +nordicom review,2 +nordicum,0 +nordina,1 +nordiques,1 +nordisk administrativt tidsskrift,1 +nordic studies on alcohol and drugs,1 +nordisk judaistik / scandinavian jewish studies,2 +nordisk kulturpolitisk tidskrift,1 +nomad: nordisk matematikkdidaktikk,1 +nordisk miljörättslig tidskrift,1 +nordisk museologi,1 +nordisk numismatisk årsskrift - scandinavian numismatic journal,1 +nordisk oestforum,1 +nordisk samhällsgeografisk tidskrift,1 +nordisk tidskrift for horsel- och dovundervisning ntd,1 +"nordisk tidskrift for vetenskap, konst och industri",1 +nordisk tidsskrift for helseforskning,1 +nordisk tidsskrift for kriminalvidenskab,1 +nordic journal of human rights,2 +nordisk tidsskrift for selskabsret,1 +"nordiske fortidsminder, serie b",1 +nordiske organisasjonsstudier,1 +nordiske udkast,1 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lights: film and media studies yearbook,1 +northern mariner,1 +northern review,1 +northern studies: the journal of the scottish society for northern studies,1 +north-west passage,1 +northwestern journal of law and social policy,1 +north-western journal of zoology,1 +northwestern university law review,2 +norwegian archaeological review,2 +"norwegian journal of agricultural sciences, supplement",1 +norwegian journal of geology,1 +norwegian petroleum society: special publications,1 +nota lepidopterologica,1 +notae praehistoricae,1 +notes,1 +notes and queries,1 +notes and records of the royal society,1 +notes on number theory and discrete mathematics,1 +notfall und rettungsmedizin,1 +abstracts of papers presented to the american mathematical society,1 +notre dame journal of formal logic,2 +notre dame law review,1 +notre dame philosophical reviews,0 +nottingham french studies,2 +nous,3 +philosophical issues: a supplement to nous,2 +nouvelle revue d'onomastique,1 +nouvelle revue francaise,1 +nouvelle revue theologique,1 +nouvelles de l archeologie,1 +nouvelles questions feministes,1 +nova hedwigia,1 +nova religio: journal of alternative and emergent religions,2 +nova srpska politicka misao,1 +nova tellus,1 +novaâ i novejsaâ istoriâ,1 +novartis foundation symposia,1 +novel: a forum on fiction,3 +nowele: north western european language evolution,1 +novenytermeles,1 +novoe literaturnoe obozrenie,2 +novon,1 +novum testamentum,3 +novus studies in literature,1 +novyi filologicheskii vestnik,1 +"ntm journal of history of sciences, technology, and medicine",1 +nuance: the international journal of family policy and related issues,1 +nuclear data sheets,1 +nuclear engineering and design,3 +nuclear engineering and technology,1 +nuclear engineering international,1 +nuclear fusion,2 +"nuclear instruments and methods in physics research section a: accelerators, spectrometers, detectors and associated equipment",1 +nuclear instruments and methods in physics research section b: beam interactions with materials and atoms,2 +nuclear medicine and biology,1 +nuclear medicine communications,1 +nuclear physics a,1 +nuclear physics b,2 +nuclear plant journal,1 +nuclear science and engineering,1 +nuclear science and techniques,1 +nuclear technology,1 +nuclear technology and radiation protection,1 +nucleic acids research,3 +nucleosides nucleotides and nucleic acids,1 +nueva antropologia,1 +nueva revista de filologia hispanica,1 +nuevo texto critico,1 +nuklearmedizin-nuclear medicine,1 +nukleonika,1 +numen: revista de estudos e pesquisa da religiao,1 +numen,3 +numerical algorithms,2 +numerical functional analysis and optimization,1 +numerical heat transfer part a: applications,1 +numerical heat transfer part b: fundamentals,1 +numerical linear algebra with applications,1 +numerical mathematics: theory methods and applications,1 +numerical methods for partial differential equations,1 +numerische mathematik,3 +numismatiska meddelanden,1 +nuncius: journal of the history of science,2 +nuorisotutkimus,1 +nuorisotutkimusverkoston verkkojulkaisuja,1 +nuova rivista musicale italiana,1 +nuova rivista storica,1 +nuova storia contemporanea,1 +il nuovo cimento c,1 +nurse education in practice,1 +nurse education today,2 +nurse educator,1 +nurse researcher,1 +nursing and health sciences,1 +nursing administration quarterly,1 +nursing clinics of north america,1 +nursing economics,1 +nursing education perspectives,1 +nursing ethics,3 +nursing history review,1 +nursing in critical care,1 +nursing inquiry,1 +nursing management,1 +nursing outlook,2 +nursing philosophy,1 +nursing praxis in new zealand,1 +nursing research,3 +nursing science quarterly,1 +nutricion hospitalaria,1 +nutrient cycling in agroecosystems,1 +nutrition,1 +nutrition and dietetics,1 +nutrition and metabolism,1 +nutrition and cancer: an international journal,1 +nutrition bulletin,1 +nutrition clinique et metabolisme,1 +nutrition in clinical practice,1 +nutrition journal,1 +nutrition metabolism and cardiovascular diseases,1 +nutrition research,1 +nutrition research and practice,1 +nutrition research reviews,1 +nutrition reviews,1 +nutritional neuroscience,1 +feminist formations,1 +nyame akuma: bulletin of the society of african archaeologists,1 +nydanske studier,1 +nyelv- es irodalomtudomanyi kozlemenyek,1 +nyelvtudomanyi kozlemenyek,1 +nykykulttuurin tutkimuskeskuksen julkaisuja,1 +nytt norsk tidsskrift,1 +opd restauro: rivista dell opificio delle pietre dure e laboratori di restauro di firenze,1 +oase: tijdschrift voor architectuur,1 +oberwolfach reports,1 +obesity,1 +obesity facts,1 +obesity research and clinical practice,1 +obesity reviews,1 +obesity surgery,2 +observatory,1 +obstetrical and gynecological survey,1 +obstetrics and gynecology,3 +obstetrics and gynecology clinics of north america,1 +occasional papers in archaeology,1 +occupational and environmental medicine,3 +occupational ergonomics,1 +occupational medicine: oxford,1 +occupational therapy in health care,1 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journal of performance and art,2 +pajouhesh va sazandegi,0 +participations: journal of audience and reception studies,1 +pastoralism,1 +pattern recognition and image analysis,0 +peer-to-peer networking and applications,1 +performing ethos: an international journal of ethics in theatre & performance,1 +perichoresis,1 +perspectives on history,0 +perspectives on performance,0 +pharmaceutics,1 +philosophy and theology,1 +philosophy of photography,1 +photonics letters of poland,0 +photosynthetica,1 +physica scripta: topical issues,1 +physical communication,1 +physics of particles and nuclei letters,1 +physics procedia,1 +phytochemistry reviews,1 +pirandelliana: rivista internazionale di studi e documenti,1 +place branding and public diplomacy,1 +plant molecular biology,1 +porin taidemuseon julkaisuja,0 +positioning,0 +posiva working report,0 +post: a review of poetry studies,0 +power and education,1 +hospital pharmacy europe,0 +primary care diabetes,1 +prime research on education,0 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engineering,0 +business research quarterly,1 +hiiskuttua,0 +entrepreneurship and sustainability issues,0 +journal of water security,1 +journal of extreme events,1 +journal of business management and economics,0 +asia-pacific journal of oncology nursing,1 +mk nambyar saarclaw review,0 +journal of materials science and nanotechnology,0 +international journal of social sciences and humanities invention,0 +international journal of innovation and research in educational sciences,1 +current opinion in psychology,1 +journal of insects as food and feed,1 +open data journal for agricultural research,0 +sustainable water resources management,1 +international journal of ethics education,1 +topics in current chemistry,1 +proceedings of the hamburg international conference of logistics,0 +lecture notes in civil engineering,1 +chemphotochem,1 +"the minerals, metals & materials series",0 +sgem international multidisciplinary scientific conferences on social sciences and arts,0 +international journal 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papers,-1 +ope journal,-1 +shareholder activism & engagement,-1 +literacy today,-1 +room,-1 +l'obs,-1 +conference proceedings,-1 +journal nano science and technology,-1 +the conversation,-1 +educitec,-1 +harbours review,-1 +compliance,-1 +surdus historicus,-1 +ancient history magazine,-1 +pööning,-1 +nordic perspectives on open science,-1 +bioinquirer journal,-1 +esrb working paper series,-1 +the arkansas international,-1 +fulbright finland news,-1 +tiedeblogi,-1 +pieni on suurin,-1 +tuiran suuralueen kuohut,-1 +pälstidskrift,-1 +loimu,-1 +xamk tutkii,-1 +xamk kehittää,-1 +xamk inspiroi,-1 +sosten julkaisuja,-1 +vaasan yliopiston raportteja,-1 +julkaisusarja,-1 +suomen sahayrittäjät,-1 +kurjenpolvet,-1 +suomen arkeoastronomisen seuran julkaisuja,-1 +tekninen tiedote,-1 +geotechnical report,-1 +holkki,-1 +eom,-1 +schuman papers,-1 +oulun yliopiston kerttu saalasti instituutin julkaisuja,-1 +reports on scientific computing and optimization,-1 +kupoli,-1 +julkaisuja,-1 +centria bulletin,-1 +aivoterveys,-1 +ikä nyt!,-1 +suomenopettajat,-1 +ham - helsingin taidemuseon julkaisuja,-1 +ympäristö & yritys tänään,-1 +lecture notes,-1 +shakki,-1 +valterin julkaisusarja,-1 +luston julkaisuja,-1 +kaupunkiympäristön julkaisuja,-1 +next,-1 +ajan kohina,-1 +muovaaja,-1 +imperiumi,-1 +kiinteistöviesti,-1 +lastensuojelun keskusliiton verkkojulkaisu,-1 +dimecc publications series,-1 +suomalaiset euroopassa,-1 +lilja,-1 +seniorilääkäri,-1 +risteysasema,-1 +i rågens och fjärdarnas rike,-1 +kansalaisareenan julkaisuja,-1 +elm magazine,-1 +fenestra finnorum,-1 +tekijä,-1 +poverty and development working papers,-1 +kulttuurista perinnöksi,-1 +tilitoimistossa,-1 +pedanssi,-1 +lousi,-1 +suek ry,-1 +yrittävä lakeus,-1 +kohtaamisia,-1 +suomen rahahistoria,-1 +arkkitehtuuri,-1 +maatilalla,-1 +birdlife,-1 +digibarometri,-1 +kansallisarkiston toimituksia,-1 +poliittiset kuplat,-1 +"allergia, iho & astma",-1 +taidetutka,-1 +pioni-jäsenlehti,-1 +studio publication,-1 +liikkeessä yli rajojen,-1 +"rengas-, varaosa- ja korjaamouutiset",-1 +biohub annual,-1 +talk magazine,-1 +kihun julkaisusarja,-1 +antroblogi,-1 +varhaiskasvatuksen erityisopettaja,-1 +julkaisusarja,-1 +kuntoutusta kehittämässä,-1 +sam magazine,-1 +acta diurna obscura,-1 +työraportteja,-1 +abc plastics news,-1 +tammenlastuja,-1 +kalmistopiiri,-1 +arbetarbladet,-1 +evento,-1 +ilmiö,-1 +valtion nuorisoneuvoston julkaisuja,-1 +näyttövinkki,-1 +ptt raportteja,-1 +kunnallisalan kehittämissäätiön julkaisu,-1 +laurea journal,-1 +ptt työpapereita,-1 +siun soten julkaisuja,-1 +nokia ennen ja nyt,-1 +dialogi,-1 +nokturno,-1 +sesko vuosikirja,-1 +lapuan joulu,-1 +ruokaviraston tutkimuksia,-1 +ruokaviraston julkaisuja,-1 +rajansiirtäjä,-1 +mediataito,-1 +ilmiö,-1 +valtioneuvoston julkaisuja,-1 +sisäministeriön julkaisuja,-1 +ympäristöministeriön julkaisuja,-1 +oikeusministeriön julkaisuja,-1 +oikeusministeriön julkaisuja,-1 +väyläviraston julkaisuja,-1 +cyberwatch magazine,-1 +valtioneuvoston kanslian julkaisuja,-1 +lajiluettelo,-1 +maan suola,-1 +väyläviraston tutkimuksia,-1 +hybrid coe strategic analysis,-1 +aamuposti viikko,-1 +folk och musik,-1 +interact,-1 +tutkimuseettisen neuvottelukunnan julkaisuja,-1 +prospäkkäri,-1 +vastuullinen tiede,-1 +oamk_kone with passion,-1 +metropolia ammattikorkeakoulun julkaisuja,-1 +the progressive post,-1 +medizinethnologie,-1 +future farming,-1 +a line which forms a volume,-1 +open access government,-1 +another gaze,-1 +research outreach,-1 +pflege professionell,-1 +fachblatt des berufsverbandes österreichischer kunst- und werkerzieherinnen,-1 +global dialogue,-1 +normal,-1 +human security,-1 +journal of the royal new zealand air force,-1 +boletín del observatorio de comercio internacional,-1 +new angle,-1 +proceedings of the teaching and education conferences,-1 +ealthy magazine,-1 +journal of patient care,-1 +phile,-1 +northeast journal of complex systems,-1 +mitmekeelne haridus,-1 +guidelines,-1 +desde el margen,-1 +world sustainable energy days,-1 +socialnet international,-1 +social europe,-1 +futurum,-1 +non-fiction,-1 +metropolia ammattikorkeakoulun julkaisuja,-1 +metropolia ammattikorkeakoulun julkaisuja,-1 +artikkelikokoelma,-1 +kansalaisuuden kuilut ja kuplat,-1 +unit,-1 +"tampereen yliopisto, rakennustekniikka",-1 +uefdsa newspaper,-1 +opeopiskelija,-1 +creating leadership,-1 +kiekaus,-1 +vaikutuksessa-media,-1 +trivium,-1 +6g research visions,-1 +raportti,-1 +pohjois-savon sotaveteraanipiirin jouluviesti,-1 +novia publikation och produktion,-1 +vastuullisen tieteen julkaisusarja,-1 +propelli,-1 +lepakot,-1 +museopro,-1 +oikeuden perusteet,-1 +ilkka-pohjalainen,-1 +eläintaudit suomessa,-1 +tem toimialaraportit,-1 +infektioidentorjunta,-1 +ihmisoikeuskeskuksen julkaisuja,-1 +6g waves,-1 +lab pro,-1 +urbaria summaries series,-1 +pro houtskär,-1 +metsäalan ammattilehti,-1 +oulun ammattikorkeakoulun tekniikan ja luonnonvara-alan lehti,-1 +muova education,-1 +kauppakamari,-1 +kauppakamari,-1 +itla research,-1 +hssh reports and working papers,-1 +business & society,-1 +eesti kunstimuuseum,-1 +noēma,-1 +outsourcing journal,-1 +new age in russia,-1 +n-iussp,-1 +the adriatic report,-1 +tallinna tervishoiu kõrgkooli väljaanded,-1 +hbl junior,-1 +neurohoitaja,-1 +kognitiivis-analyyttisen psykoterapiayhdistyksen julkaisuja,-1 +modus 3d journal,-1 +energiaa,-1 +esignals pro,-1 +esignals,-1 +sähkömaailma extra,-1 +näkökulma,-1 +luonnosta sinulle,-1 +tutkimuksia,-1 +kotikulmilta,-1 +dynamic interpretations of the past,-1 +verde,-1 +jyu reports,-1 +toiminta soi,-1 +kinestetiikka,-1 +invest working papers,-1 +oamk journal,-1 +julkaisusarja,-1 +raportti,-1 +hybrid coe research report,-1 +sosiaalitieteiden laitoksen julkaisuja,-1 +suomen ilmastopaneelin julkaisuja,-1 +botnia insider,-1 +pohjolan historiankirjoitus,-1 +helsus policy brief,-1 +pulssi-portaali,-1 +novissima,-1 +perhe- ja pariterapialehti,-1 +diak publications,-1 +"the heppsinki working papers on emotions, populism and polarisation",-1 +tutkittua varhaiskasvatuksesta,-1 +sateenkaarihistorian ystävien kirjoituksia,-1 +school education gateway,-1 +социодиггер,-1 +casas internacional,-1 +policy options,-1 +inroads,-1 +landskab,-1 +practicus,-1 +tenen,-1 +dragtjournalen,-1 +altinget,-1 +ulevaade haridussusteemi valishindamisest,-1 +kuidas korraldada kultuuri?,-1 +vikerkaar,-1 +raduga,-1 +kuntalehti,-1 +liha ja ruoka,-1 +signals,-1 +tekstiililehti,-1 +konservaattori,-1 +leipuri,-1 +nukketeatteri,-1 +puuviesti.fi,-1 +suomen autolehti,-1 +tamkjournal (english ed.),-1 +varsinais-suomen yrittäjä,-1 +kirkkomme lähetys,-1 +metsä groupin viesti,-1 +panssari,-1 +poromies,-1 +syöpäsairaanhoitaja,-1 +talouselämä,-1 +#tyottomat,-1 +analyytikko,-1 +arkkitehtiuutiset,-1 +avain,-1 +biokierto ja biokaasu,-1 +diakonia+,-1 +eliksiiri,-1 +geofoor,-1 +hammasteknikko,-1 +juristiuutiset,-1 +kantele,-1 +kasvinsuojelulehti,-1 +kemia,-1 +kielikello,-1 +kiinteistö ja energia,-1 +puutarhakalenteri,-1 +suomi merellä,-1 +suomen kotiseutuliiton julkaisusarja,-1 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d'entreprise magazine,-1 +ehne,-1 +le grand continent,-1 +analyse opinion critique,-1 +atlantico,-1 +nachrichten der arl,-1 +leibniz online,-1 +zeitzeichen,-1 +marketing intelligence review (english ed.),-1 +denken ohne geländer,-1 +zeit germany : work & start up,-1 +zeit-magazin,-1 +marketing intelligence review,-1 +kanbrief,-1 +die zeit,-1 +zeit germany : study & research,-1 +zeitmagazin,-1 +nea ygeia,-1 +szombat,-1 +"testing, evaluation and assessment today",-1 +iatefl voices,-1 +ndc policy brief,-1 +past global changes magazine,-1 +ifla metadata newsletter,-1 +childlinks,-1 +alimenta,-1 +jlis.it,-1 +mindbrained bulletin,-1 +subaru,-1 +ancient warfare,-1 +nytt om namn,-1 +adresseavisen,-1 +dawn,-1 +gazeta wyborcza,-1 +put i saobraćaj,-1 +sårjournalen,-1 +eyvind johnson-sällskapets årsbok,-1 +studiehäfte till årsboken horisont,-1 +läs- och skrivsvårigheter & dyslexi,-1 +värmland förr och nu,-1 +till liv,-1 +c'est bon,-1 +horisont,-1 +vuosi,-1 +western europe,-1 +the integrated review in context,-1 +epilepsy professional,-1 +international environmental technology,-1 +frontiers of socio-legal studies,-1 +the national interest,-1 +the gradient,-1 +cal lab,-1 +clarity,-1 +healthcare design,-1 +conference proceedings : international conference on unmanned aircraft systems,-1 +sport supplement,-1 diff --git a/paperqa/clients/client_models.py b/paperqa/clients/client_models.py new file mode 100644 index 00000000..bdb8b254 --- /dev/null +++ b/paperqa/clients/client_models.py @@ -0,0 +1,166 @@ +from __future__ import annotations + +import logging +from abc import ABC, abstractmethod +from typing import Any, Collection, Generic, TypeVar + +import aiohttp +from pydantic import ( + BaseModel, + ConfigDict, + ValidationError, + ValidationInfo, + field_validator, + model_validator, +) + +from paperqa.clients.exceptions import DOINotFoundError + +from ..types import DocDetails + +logger = logging.getLogger(__name__) + + +# ClientQuery is a base class for all queries to the client_models +class ClientQuery(BaseModel): + session: aiohttp.ClientSession + model_config = ConfigDict(arbitrary_types_allowed=True) + + +class TitleAuthorQuery(ClientQuery): + title: str + authors: list[str] = [] + title_similarity_threshold: float = 0.75 + fields: Collection[str] | None = None + + @model_validator(mode="before") + @classmethod + def ensure_fields_are_present(cls, data: dict[str, Any]) -> dict[str, Any]: + if fields := data.get("fields"): + if "doi" not in fields: + fields.append("doi") + if "title" not in fields: + fields.append("title") + if data.get("authors") is not None and "authors" not in fields: + fields.append("authors") + # ensure these are ranked the same for caching purposes + data["fields"] = sorted(fields) + return data + + @field_validator("title_similarity_threshold") + @classmethod + def zero_and_one(cls, v: float, info: ValidationInfo) -> float: # noqa: ARG003 + if v < 0.0 or v > 1.0: + raise ValueError( + "title_similarity_threshold must be between 0 and 1. (inclusive)" + ) + return v + + +class DOIQuery(ClientQuery): + doi: str + fields: Collection[str] | None = None + + @model_validator(mode="before") + @classmethod + def ensure_fields_are_present(cls, data: dict[str, Any]) -> dict[str, Any]: + if (fields := data.get("fields")) and "doi" not in fields: + fields.append("doi") + return data + + +class JournalQuery(ClientQuery): + journal: str + + +ClientQueryType = TypeVar("ClientQueryType", bound=ClientQuery) + + +class MetadataProvider(ABC, Generic[ClientQueryType]): + """Provide metadata from a query by any means necessary.""" + + async def query(self, query: dict) -> DocDetails | None: + return await self._query(self.query_transformer(query)) + + @abstractmethod + async def _query(self, query: ClientQueryType) -> DocDetails | None: + pass + + @abstractmethod + def query_transformer(self, query: dict) -> ClientQueryType: + pass + + +class DOIOrTitleBasedProvider(MetadataProvider[DOIQuery | TitleAuthorQuery]): + + async def query(self, query: dict) -> DocDetails | None: + try: + client_query = self.query_transformer(query) + return await self._query(client_query) + # We allow graceful failures, i.e. return "None" for both DOI errors and timeout errors + # DOINotFoundError means the paper doesn't exist in the source, the timeout is to prevent + # this service from failing us when it's down or slow. + except DOINotFoundError: + logger.exception( + f"Metadata not found for " + f"{client_query.doi if isinstance(client_query, DOIQuery) else client_query.title}" + " in Crossref." + ) + except TimeoutError: + logger.exception( + f"Request to Crossref for " + f"{client_query.doi if isinstance(client_query, DOIQuery) else client_query.title}" + " timed out." + ) + return None + + @abstractmethod + async def _query(self, query: DOIQuery | TitleAuthorQuery) -> DocDetails | None: + """ + Query the source using either a DOI or title/author search. + + None should be returned if the DOI or title is not a good match. + + Raises: + DOINotFoundError: This is when the DOI or title is not found in the sources + TimeoutError: When the request takes too long on the client side + """ + + def query_transformer(self, query: dict) -> DOIQuery | TitleAuthorQuery: + try: + if "doi" in query: + return DOIQuery(**query) + if "title" in query: + return TitleAuthorQuery(**query) + except ValidationError as e: + raise ValueError( + f"Query {query} format not supported by {self.__class__.__name__}." + ) from e + + raise ValueError("Provider query missing 'doi' or 'title' field.") + + +class MetadataPostProcessor(ABC, Generic[ClientQueryType]): + """Post-process metadata from a query. + + MetadataPostProcessor should be idempotent and not order-dependent, i.e. + all MetadataPostProcessor instances should be able to run in parallel. + + """ + + async def process(self, doc_details: DocDetails, **kwargs) -> DocDetails: + if query := self.query_creator(doc_details, **kwargs): + return await self._process(query, doc_details) + return doc_details + + @abstractmethod + async def _process( + self, query: ClientQueryType, doc_details: DocDetails + ) -> DocDetails: + pass + + @abstractmethod + def query_creator( + self, doc_details: DocDetails, **kwargs + ) -> ClientQueryType | None: + pass diff --git a/paperqa/clients/crossref.py b/paperqa/clients/crossref.py new file mode 100644 index 00000000..7e587514 --- /dev/null +++ b/paperqa/clients/crossref.py @@ -0,0 +1,344 @@ +from __future__ import annotations + +import copy +import json +import logging +import os +from datetime import datetime +from typing import Any, Collection +from urllib.parse import quote + +import aiohttp + +from ..clients.exceptions import DOINotFoundError +from ..types import CITATION_FALLBACK_DATA, DocDetails +from ..utils import ( + bibtex_field_extract, + remove_substrings, + strings_similarity, + union_collections_to_ordered_list, +) +from .client_models import DOIOrTitleBasedProvider, DOIQuery, TitleAuthorQuery + +logger = logging.getLogger(__name__) + +CROSSREF_BASE_URL = "https://api.crossref.org" +CROSSREF_HEADER_KEY = "Crossref-Plus-API-Token" +CROSSREF_API_REQUEST_TIMEOUT = 5.0 +CROSSREF_API_MAPPING: dict[str, Collection[str]] = { + "title": {"title"}, + "doi": {"DOI"}, + "authors": {"author"}, + "publication_date": {"published"}, + "year": {"published"}, + "volume": {"volume"}, + "issue": {"issue"}, + "publisher": {"publisher"}, + "issn": {"ISSN"}, + "pages": {"page"}, + "journal": {"container-title"}, + "doi_url": {"URL"}, + "url": {"URL"}, + "bibtex": {"bibtex", "type"}, + "citation_count": {"is-referenced-by-count"}, + "bibtex_type": {"type"}, + "citation": { + "title", + "DOI", + "published", + "volume", + "issue", + "publisher", + "ISSN", + "page", + "container-title", + "is-referenced-by-count", + "type", + }, + "source_quality": {"container-title"}, + "doc_id": {"DOI"}, +} +CROSSREF_CONTENT_TYPE_TO_BIBTEX_MAPPING: dict[str, str] = { + "journal-article": "article", + "journal-issue": "misc", # No direct equivalent, so 'misc' is used + "journal-volume": "misc", # No direct equivalent, so 'misc' is used + "journal": "misc", # No direct equivalent, so 'misc' is used + "proceedings-article": "inproceedings", + "proceedings": "proceedings", + "dataset": "misc", # No direct equivalent, so 'misc' is used + "component": "misc", # No direct equivalent, so 'misc' is used + "report": "techreport", + "report-series": "techreport", # 'series' implies multiple tech reports, but each is still a 'techreport' + "standard": "misc", # No direct equivalent, so 'misc' is used + "standard-series": "misc", # No direct equivalent, so 'misc' is used + "edited-book": "book", # Edited books are considered books in BibTeX + "monograph": "book", # Monographs are considered books in BibTeX + "reference-book": "book", # Reference books are considered books in BibTeX + "book": "book", + "book-series": "book", # Series of books can be considered as 'book' in BibTeX + "book-set": "book", # Set of books can be considered as 'book' in BibTeX + "book-chapter": "inbook", + "book-section": "inbook", # Sections in books can be considered as 'inbook' + "book-part": "inbook", # Parts of books can be considered as 'inbook' + "book-track": "inbook", # Tracks in books can be considered as 'inbook' + "reference-entry": "inbook", # Entries in reference books can be considered as 'inbook' + "dissertation": "phdthesis", # Dissertations are usually PhD thesis + "posted-content": "misc", # No direct equivalent, so 'misc' is used + "peer-review": "misc", # No direct equivalent, so 'misc' is used + "other": "article", # Assume an article if we don't know the type +} + + +def crossref_headers() -> dict[str, str]: + """Crossref API key if available, otherwise nothing.""" + if api_key := os.environ.get("CROSSREF_API_KEY"): + return {CROSSREF_HEADER_KEY: f"Bearer {api_key}"} + logger.warning( + "CROSSREF_API_KEY environment variable not set. Crossref API rate limits may apply." + ) + return {} + + +async def doi_to_bibtex( + doi: str, + session: aiohttp.ClientSession, + missing_replacements: dict[str, str] | None = None, +) -> str: + """Get a bibtex entry from a DOI via Crossref, replacing the key if possible. + + `missing_replacements` can optionally be used to fill missing fields in the bibtex key. + these fields are NOT replaced or inserted into the bibtex string otherwise. + + """ + if missing_replacements is None: + missing_replacements = {} + FORBIDDEN_KEY_CHARACTERS = {"_", " ", "-", "/"} + # get DOI via crossref + url = f"https://api.crossref.org/works/{quote(doi, safe='')}/transform/application/x-bibtex" + async with session.get(url, headers=crossref_headers()) as r: + if not r.ok: + raise DOINotFoundError( + f"Per HTTP status code {r.status}, could not resolve DOI {doi}." + ) + data = await r.text() + # must make new key + key = data.split("{")[1].split(",")[0] + new_key = remove_substrings(key, FORBIDDEN_KEY_CHARACTERS) + substrings_to_remove_per_field = {"author": [" and ", ","]} + fragments = [ + remove_substrings( + bibtex_field_extract( + data, field, missing_replacements=missing_replacements + ), + substrings_to_remove_per_field.get(field, []), + ) + for field in ("author", "year", "title") + ] + # replace the key if all the fragments are present + if all(fragments): + new_key = remove_substrings(("".join(fragments)), FORBIDDEN_KEY_CHARACTERS) + # we use the count parameter below to ensure only the 1st entry is replaced + return data.replace(key, new_key, 1) + + +async def parse_crossref_to_doc_details( # noqa: C901 + message: dict[str, Any], + session: aiohttp.ClientSession, + query_bibtex: bool = True, +) -> DocDetails: + + bibtex_source = "self_generated" + bibtex = None + + try: + # get the title from the message, if it exists + # rare circumstance, but bibtex may not have a title + fallback_data = copy.copy(CITATION_FALLBACK_DATA) + if title := ( + None if not message.get("title") else message.get("title", [None])[0] + ): + fallback_data["title"] = title + + # TODO: we keep this for robustness, but likely not needed anymore, + # since we now create the bibtex from scratch + if query_bibtex: + bibtex = await doi_to_bibtex( + message["DOI"], session, missing_replacements=fallback_data # type: ignore[arg-type] + ) + # track the origin of the bibtex entry for debugging + bibtex_source = "crossref" + + except DOINotFoundError: + pass + + authors = [ + f"{author.get('given', '')} {author.get('family', '')}".strip() + for author in message.get("author", []) + ] + + publication_date = None + if "published" in message and "date-parts" in message["published"]: + date_parts = message["published"]["date-parts"][0] + if len(date_parts) >= 3: # noqa: PLR2004 + publication_date = datetime(date_parts[0], date_parts[1], date_parts[2]) + elif len(date_parts) == 2: # noqa: PLR2004 + publication_date = datetime(date_parts[0], date_parts[1], 1) + elif len(date_parts) == 1: + publication_date = datetime(date_parts[0], 1, 1) + + doc_details = DocDetails( # type: ignore[call-arg] + key=None if not bibtex else bibtex.split("{")[1].split(",")[0], + bibtex_type=CROSSREF_CONTENT_TYPE_TO_BIBTEX_MAPPING.get( + message.get("type", "other"), "misc" + ), + bibtex=bibtex, + authors=authors, + publication_date=publication_date, + year=message.get("published", {}).get("date-parts", [[None]])[0][0], + volume=message.get("volume"), + issue=message.get("issue"), + publisher=message.get("publisher"), + issn=message.get("ISSN", [None])[0], + pages=message.get("page"), + journal=( + None + if not message.get("container-title") + else message["container-title"][0] + ), + url=message.get("URL"), + title=None if not message.get("title") else message.get("title", [None])[0], + citation_count=message.get("is-referenced-by-count"), + doi=message.get("DOI"), + other={}, # Initialize empty dict for other fields + ) + + # Add any additional fields to the 'other' dict + for key, value in ( + message | {"client_source": ["crossref"], "bibtex_source": [bibtex_source]} + ).items(): + if key not in doc_details.model_fields: + if key in doc_details.other: + doc_details.other[key] = [doc_details.other[key], value] + else: + doc_details.other[key] = value + + return doc_details + + +async def get_doc_details_from_crossref( # noqa: C901, PLR0912 + session: aiohttp.ClientSession, + doi: str | None = None, + authors: list[str] | None = None, + title: str | None = None, + title_similarity_threshold: float = 0.75, + fields: Collection[str] | None = None, +) -> DocDetails | None: + """ + Get paper details from Crossref given a DOI or paper title. + + SEE: https://api.crossref.org/swagger-ui/index.html#/Works + """ + if authors is None: + authors = [] + if doi is title is None: + raise ValueError("Either a DOI or title must be provided.") + if doi is not None and title is not None: + title = None # Prefer DOI over title + + inputs_msg = f"DOI {doi}" if doi is not None else f"title {title}" + + if not (CROSSREF_MAILTO := os.getenv("CROSSREF_MAILTO")): + logger.warning( + "CROSSREF_MAILTO environment variable not set. Crossref API rate limits may apply." + ) + CROSSREF_MAILTO = "test@example.com" + quoted_doi = f"/{quote(doi, safe='')}" if doi else "" + url = f"{CROSSREF_BASE_URL}/works{quoted_doi}" + params = {"mailto": CROSSREF_MAILTO} + if title: + params.update({"query.title": title, "rows": "1"}) + + if authors: + params.update( + {"query.author": " ".join([a.strip() for a in authors if len(a) > 1])} + ) + + query_bibtex = True + + if fields: + # crossref has a special endpoint for bibtex, so we don't need to request it here + if "bibtex" not in fields: + query_bibtex = False + params.update( + { + "select": ",".join( + union_collections_to_ordered_list( + [ + CROSSREF_API_MAPPING[field] + for field in fields + if field in CROSSREF_API_MAPPING and field != "bibtex" + ] + ) + ) + } + ) + + async with session.get( + url, + params=params, + headers=crossref_headers(), + timeout=aiohttp.ClientTimeout(CROSSREF_API_REQUEST_TIMEOUT), + ) as response: + try: + response.raise_for_status() + except aiohttp.ClientResponseError as exc: + raise DOINotFoundError(f"Could not find paper given {inputs_msg}.") from exc + try: + response_data = await response.json() + except json.JSONDecodeError as exc: + # JSONDecodeError: Crossref didn't answer with JSON, perhaps HTML + raise DOINotFoundError( # Use DOINotFoundError so we fall back to Google Scholar + f"Crossref API did not return JSON for {inputs_msg}, instead it" + f" responded with text: {await response.text()}" + ) from exc + if response_data["status"] == "failed": + raise DOINotFoundError( + f"Crossref API returned a failed status for {inputs_msg}." + ) + message: dict[str, Any] = response_data["message"] + # restructure data if it comes back as a list result + # it'll also be a list if we searched by title and it's empty + if "items" in message: + try: + message = message["items"][0] + except IndexError as e: + raise DOINotFoundError( + f"Crossref API did not return any items for {inputs_msg}." + ) from e + # since score is not consistent between queries, we need to rely on our own criteria + # title similarity must be > title_similarity_threshold + if ( + doi is None + and title + and strings_similarity(message["title"][0], title) < title_similarity_threshold + ): + raise DOINotFoundError(f"Crossref results did not match for title {title!r}.") + if doi is not None and message["DOI"] != doi: + raise DOINotFoundError(f"DOI ({inputs_msg}) not found in Crossref") + + return await parse_crossref_to_doc_details(message, session, query_bibtex) + + +class CrossrefProvider(DOIOrTitleBasedProvider): + async def _query(self, query: TitleAuthorQuery | DOIQuery) -> DocDetails | None: + if isinstance(query, DOIQuery): + return await get_doc_details_from_crossref( + doi=query.doi, session=query.session, fields=query.fields + ) + return await get_doc_details_from_crossref( + title=query.title, + authors=query.authors, + session=query.session, + title_similarity_threshold=query.title_similarity_threshold, + fields=query.fields, + ) diff --git a/paperqa/clients/exceptions.py b/paperqa/clients/exceptions.py new file mode 100644 index 00000000..09178aa1 --- /dev/null +++ b/paperqa/clients/exceptions.py @@ -0,0 +1,4 @@ +class DOINotFoundError(Exception): + def __init__(self, message="DOI not found"): + self.message = message + super().__init__(self.message) diff --git a/paperqa/clients/journal_quality.py b/paperqa/clients/journal_quality.py new file mode 100644 index 00000000..2d9580a4 --- /dev/null +++ b/paperqa/clients/journal_quality.py @@ -0,0 +1,57 @@ +from __future__ import annotations + +import csv +import logging +import os +from typing import Any + +from pydantic import ValidationError + +from ..types import DocDetails +from .client_models import JournalQuery, MetadataPostProcessor + +logger = logging.getLogger(__name__) + + +# TODO: refresh script for journal quality data + + +class JournalQualityPostProcessor(MetadataPostProcessor[JournalQuery]): + def __init__(self, journal_quality_path: os.PathLike | str | None = None) -> None: + if journal_quality_path is None: + # Construct the path relative to module + self.journal_quality_path = str( + os.path.join( + os.path.dirname(__file__), "client_data", "journal_quality.csv" + ) + ) + else: + self.journal_quality_path = str(journal_quality_path) + self.data: dict[str, Any] | None = None + + def load_data(self) -> None: + self.data = {} + with open(self.journal_quality_path, newline="", encoding="utf-8") as csvfile: + for row in csv.DictReader(csvfile): + self.data[row["clean_name"]] = int(row["quality"]) + + async def _process( + self, query: JournalQuery, doc_details: DocDetails + ) -> DocDetails: + if not self.data: + self.load_data() + # docname can be blank since the validation will add it + # remember, if both have docnames (i.e. key) they are + # wiped and re-generated with resultant data + return doc_details + DocDetails( # type: ignore[call-arg] + source_quality=self.data.get(query.journal.casefold(), -1) # type: ignore[union-attr] + ) + + def query_creator(self, doc_details: DocDetails, **kwargs) -> JournalQuery | None: + try: + return JournalQuery(journal=doc_details.journal, **kwargs) + except ValidationError: + logger.debug( + "Must have a valid journal name to query journal quality data." + ) + return None diff --git a/paperqa/clients/semantic_scholar.py b/paperqa/clients/semantic_scholar.py new file mode 100644 index 00000000..d11fc9cb --- /dev/null +++ b/paperqa/clients/semantic_scholar.py @@ -0,0 +1,319 @@ +from __future__ import annotations + +import logging +import os +from datetime import datetime +from enum import IntEnum, auto +from http import HTTPStatus +from itertools import starmap +from typing import Any, Collection + +import aiohttp + +from ..types import DocDetails +from ..utils import ( + _get_with_retrying, + clean_upbibtex, + strings_similarity, + union_collections_to_ordered_list, +) +from .client_models import DOIOrTitleBasedProvider, DOIQuery, TitleAuthorQuery +from .crossref import doi_to_bibtex +from .exceptions import DOINotFoundError + +logger = logging.getLogger(__name__) + +# map from S2 fields to those in the DocDetails model +# allows users to specify which fields to include in the response +SEMANTIC_SCHOLAR_API_MAPPING: dict[str, Collection[str]] = { + "title": {"title"}, + "doi": {"externalIds"}, + "authors": {"authors"}, + "publication_date": {"publicationDate"}, + "year": {"year"}, + "volume": {"journal"}, + "pages": {"journal"}, + "journal": {"journal"}, + "url": {"url", "openAccessPdf"}, + "bibtex": {"citationStyles"}, + "doi_url": {"url"}, + "other": {"isOpenAccess", "influentialCitationCount", "publicationTypes", "venue"}, + "citation_count": {"citationCount"}, + "source_quality": {"journal"}, +} +SEMANTIC_SCHOLAR_API_REQUEST_TIMEOUT = 10.0 +SEMANTIC_SCHOLAR_API_FIELDS: str = ",".join( + union_collections_to_ordered_list(SEMANTIC_SCHOLAR_API_MAPPING.values()) +) +SEMANTIC_SCHOLAR_BASE_URL = "https://api.semanticscholar.org" +SEMANTIC_SCHOLAR_HEADER_KEY = "x-api-key" + + +class SematicScholarSearchType(IntEnum): + DEFAULT = auto() + PAPER = auto() + PAPER_RECOMMENDATIONS = auto() + DOI = auto() + FUTURE_CITATIONS = auto() + PAST_REFERENCES = auto() + GOOGLE = auto() + MATCH = auto() + + def make_url_params( # noqa: PLR0911 + self, + params: dict[str, Any], + query: str = "", + offset: int = 0, + limit: int = 1, + include_base_url: bool = True, + ) -> tuple[str, dict[str, Any]]: + """ + Make the target URL and in-place update the input URL parameters. + + Args: + params: URL parameters to in-place update. + query: Either a search query or a Semantic Scholar paper ID. + offset: Offset to place in the URL parameters for the default search type. + limit: Limit to place in the URL parameters for some search types. + include_base_url: Set True (default) to include the base URL. + + Returns: + Two-tuple of URL and URL parameters. + """ + base = SEMANTIC_SCHOLAR_BASE_URL if include_base_url else "" + if self == SematicScholarSearchType.DEFAULT: + params["query"] = query.replace("-", " ") + params["offset"] = offset + params["limit"] = limit + return f"{base}/graph/v1/paper/search", params + if self == SematicScholarSearchType.PAPER: + return f"{base}/graph/v1/paper/{query}", params + if self == SematicScholarSearchType.PAPER_RECOMMENDATIONS: + return f"{base}/recommendations/v1/papers/forpaper/{query}", params + if self == SematicScholarSearchType.DOI: + return f"{base}/graph/v1/paper/DOI:{query}", params + if self == SematicScholarSearchType.FUTURE_CITATIONS: + params["limit"] = limit + return f"{base}/graph/v1/paper/{query}/citations", params + if self == SematicScholarSearchType.PAST_REFERENCES: + params["limit"] = limit + return f"{base}/graph/v1/paper/{query}/references", params + if self == SematicScholarSearchType.GOOGLE: + params["limit"] = 1 + return f"{base}/graph/v1/paper/search", params + if self == SematicScholarSearchType.MATCH: + return f"{base}/graph/v1/paper/search/match", params + raise NotImplementedError + + +def s2_authors_match(authors: list[str], data: dict): + """Check if the authors in the data match the authors in the paper.""" + AUTHOR_NAME_MIN_LENGTH = 2 + s2_authors_noinit = [ + " ".join([w for w in a["name"].split() if len(w) > AUTHOR_NAME_MIN_LENGTH]) + for a in data["authors"] + ] + authors_noinit = [ + " ".join([w for w in a.split() if len(w) > AUTHOR_NAME_MIN_LENGTH]) + for a in authors + ] + # Note: we expect the number of authors to be possibly different + return any( + starmap( + lambda x, y: x in y or y in x, + zip(s2_authors_noinit, authors_noinit, strict=False), + ) + ) + + +async def parse_s2_to_doc_details( + paper_data: dict, session: aiohttp.ClientSession +) -> DocDetails: + + bibtex_source = "self_generated" + + if "data" in paper_data: + paper_data = paper_data["data"][0] + + if "ArXiv" in paper_data["externalIds"]: + doi = "10.48550/arXiv." + paper_data["externalIds"]["ArXiv"] + elif "DOI" in paper_data["externalIds"]: + doi = paper_data["externalIds"]["DOI"] + else: + raise DOINotFoundError(f"Could not find DOI for {paper_data}.") + + # Should we give preference to auto-generation? + if not ( + bibtex := clean_upbibtex(paper_data.get("citationStyles", {}).get("bibtex", "")) + ): + try: + bibtex = await doi_to_bibtex(doi, session) + bibtex_source = "crossref" + except DOINotFoundError: + bibtex = None + else: + bibtex_source = "semantic_scholar" + + publication_date = None + if paper_data.get("publicationDate"): + publication_date = datetime.strptime(paper_data["publicationDate"], "%Y-%m-%d") + + doc_details = DocDetails( # type: ignore[call-arg] + key=None if not bibtex else bibtex.split("{")[1].split(",")[0], + bibtex_type="article", # s2 should be basically all articles + bibtex=bibtex, + authors=[author["name"] for author in paper_data.get("authors", [])], + publication_date=publication_date, + year=paper_data.get("year"), + volume=paper_data.get("journal", {}).get("volume"), + pages=paper_data.get("journal", {}).get("pages"), + journal=paper_data.get("journal", {}).get("name"), + url=(paper_data.get("openAccessPdf") or {}).get("url"), + title=paper_data.get("title"), + citation_count=paper_data.get("citationCount"), + doi=paper_data.get("externalIds", {}).get("DOI"), + other={}, # Initialize empty dict for other fields + ) + + # Add any additional fields to the 'other' dict + for key, value in ( + paper_data + | {"client_source": ["semantic_scholar"], "bibtex_source": [bibtex_source]} + ).items(): + if key not in doc_details.model_fields: + doc_details.other[key] = value + + return doc_details + + +def semantic_scholar_headers() -> dict[str, str]: + """Semantic Scholar API key if available, otherwise nothing.""" + if api_key := os.environ.get("SEMANTIC_SCHOLAR_API_KEY"): + return {SEMANTIC_SCHOLAR_HEADER_KEY: api_key} + logger.warning( + "SEMANTIC_SCHOLAR_API_KEY environment variable not set. Semantic Scholar API rate limits may apply." + ) + return {} + + +async def s2_title_search( + title: str, + session: aiohttp.ClientSession, + authors: list[str] | None = None, + title_similarity_threshold: float = 0.75, + fields: str = SEMANTIC_SCHOLAR_API_FIELDS, +) -> DocDetails: + """Reconcile DOI from Semantic Scholar - which only checks title. So we manually check authors.""" + if authors is None: + authors = [] + endpoint, params = SematicScholarSearchType.MATCH.make_url_params( + params={"query": title, "fields": fields} + ) + + data = await _get_with_retrying( + url=endpoint, + params=params, + session=session, + headers=semantic_scholar_headers(), + timeout=SEMANTIC_SCHOLAR_API_REQUEST_TIMEOUT, + http_exception_mappings={ + HTTPStatus.NOT_FOUND: DOINotFoundError(f"Could not find DOI for {title}.") + }, + ) + + if authors and not s2_authors_match(authors, data["data"][0]): + raise DOINotFoundError(f"Could not find DOI for {title} - author disagreement.") + # need to check if nested under a 'data' key or not (depends on filtering) + if ( + strings_similarity( + data.get("title") if "data" not in data else data["data"][0]["title"], + title, + ) + < title_similarity_threshold + ): + raise DOINotFoundError( + f"Semantic scholar results did not match for title {title!r}." + ) + return await parse_s2_to_doc_details(data, session) + + +async def get_s2_doc_details_from_doi( + doi: str | None, + session: aiohttp.ClientSession, + fields: Collection[str] | None = None, +) -> DocDetails: + """Get paper details from Semantic Scholar given a DOI.""" + # should always be string, runtime error catch + if doi is None: + raise ValueError("Valid DOI must be provided.") + + if fields: + s2_fields = ",".join( + union_collections_to_ordered_list( + SEMANTIC_SCHOLAR_API_MAPPING[f] + for f in fields + if f in SEMANTIC_SCHOLAR_API_MAPPING + ) + ) + else: + s2_fields = SEMANTIC_SCHOLAR_API_FIELDS + + details = await _get_with_retrying( + url=f"{SEMANTIC_SCHOLAR_BASE_URL}/graph/v1/paper/DOI:{doi}", + params={"fields": s2_fields}, + session=session, + headers=semantic_scholar_headers(), + timeout=SEMANTIC_SCHOLAR_API_REQUEST_TIMEOUT, + ) + + return await parse_s2_to_doc_details(details, session) + + +async def get_s2_doc_details_from_title( + title: str | None, + session: aiohttp.ClientSession, + authors: list[str] | None = None, + fields: Collection[str] | None = None, + title_similarity_threshold: float = 0.75, +) -> DocDetails: + """Get paper details from Semantic Scholar given a title. + + Optionally match against authors if provided. + """ + if title is None: + raise ValueError("Valid title must be provided.") + if authors is None: + authors = [] + if fields: + s2_fields = ",".join( + union_collections_to_ordered_list( + SEMANTIC_SCHOLAR_API_MAPPING[f] + for f in fields + if f in SEMANTIC_SCHOLAR_API_MAPPING + ) + ) + else: + s2_fields = SEMANTIC_SCHOLAR_API_FIELDS + + return await s2_title_search( + title, + authors=authors, + session=session, + title_similarity_threshold=title_similarity_threshold, + fields=s2_fields, + ) + + +class SemanticScholarProvider(DOIOrTitleBasedProvider): + async def _query(self, query: TitleAuthorQuery | DOIQuery) -> DocDetails | None: + if isinstance(query, DOIQuery): + return await get_s2_doc_details_from_doi( + doi=query.doi, session=query.session, fields=query.fields + ) + return await get_s2_doc_details_from_title( + title=query.title, + authors=query.authors, + session=query.session, + title_similarity_threshold=query.title_similarity_threshold, + fields=query.fields, + ) diff --git a/paperqa/docs.py b/paperqa/docs.py index 212e1b2e..214653f0 100644 --- a/paperqa/docs.py +++ b/paperqa/docs.py @@ -21,7 +21,7 @@ except ImportError: USE_VOYAGE = False - +from .clients import ALL_CLIENTS, DocMetadataClient from .llms import ( HybridEmbeddingModel, LLMModel, @@ -42,6 +42,7 @@ CallbackFactory, Context, Doc, + DocDetails, DocKey, LLMResult, PromptCollection, @@ -87,7 +88,7 @@ class Docs(BaseModel): ) summary_llm_model: LLMModel | None = Field(default=None, validate_default=True) embedding: str | None = "default" - docs: dict[DocKey, Doc] = {} + docs: dict[DocKey, Doc | DocDetails] = {} texts: list[Text] = [] docnames: set[str] = set() texts_index: VectorStore = Field(default_factory=NumpyVectorStore) @@ -279,6 +280,11 @@ async def aadd_file( docname: str | None = None, dockey: DocKey | None = None, chunk_chars: int = 3000, + title: str | None = None, + doi: str | None = None, + authors: list[str] | None = None, + use_doc_details: bool = False, + **kwargs, ) -> str | None: """Add a document to the collection.""" # just put in temp file and use existing method @@ -297,6 +303,11 @@ async def aadd_file( docname=docname, dockey=dockey, chunk_chars=chunk_chars, + title=title, + doi=doi, + authors=authors, + use_doc_details=use_doc_details, + **kwargs, ) def add_url( @@ -348,6 +359,11 @@ def add( disable_check: bool = False, dockey: DocKey | None = None, chunk_chars: int = 3000, + title: str | None = None, + doi: str | None = None, + authors: list[str] | None = None, + use_doc_details: bool = False, + **kwargs, ) -> str | None: loop = get_loop() return loop.run_until_complete( @@ -358,10 +374,15 @@ def add( disable_check=disable_check, dockey=dockey, chunk_chars=chunk_chars, + title=title, + doi=doi, + authors=authors, + use_doc_details=use_doc_details, + **kwargs, ) ) - async def aadd( + async def aadd( # noqa: C901, PLR0912, PLR0915 self, path: Path, citation: str | None = None, @@ -369,6 +390,11 @@ async def aadd( disable_check: bool = False, dockey: DocKey | None = None, chunk_chars: int = 3000, + title: str | None = None, + doi: str | None = None, + authors: list[str] | None = None, + use_doc_details: bool = False, + **kwargs, ) -> str | None: """Add a document to the collection.""" if dockey is None: @@ -412,7 +438,52 @@ async def aadd( year = match.group(1) docname = f"{author}{year}" docname = self._get_unique_name(docname) + doc = Doc(docname=docname, citation=citation, dockey=dockey) + + # try to extract DOI / title from the citation + if (doi is title is None) and use_doc_details: + structured_cite_chain = self.llm_model.make_chain( + client=self._client, + prompt=self.prompts.structured_cite, + skip_system=True, + ) + chain_result = await structured_cite_chain({"citation": citation}, None) + with contextlib.suppress(json.JSONDecodeError): + citation_json = json.loads(chain_result.text) + if citation_title := citation_json.get("title"): + title = citation_title + if citation_doi := citation_json.get("doi"): + doi = citation_doi + if citation_author := citation_json.get("authors"): + authors = citation_author + + # see if we can upgrade to DocDetails + # if not, we can progress with a normal Doc + # if "overwrite_fields_from_metadata" is used: + # will map "docname" to "key", and "dockey" to "doc_id" + if (title or doi) and use_doc_details: + if kwargs.get("metadata_client"): + metadata_client = kwargs["metadata_client"] + else: + metadata_client = DocMetadataClient( + session=kwargs.pop("session", None), + clients=kwargs.pop("clients", ALL_CLIENTS), + ) + + query_kwargs: dict[str, Any] = {} + + if doi: + query_kwargs["doi"] = doi + if authors: + query_kwargs["authors"] = authors + if title: + query_kwargs["title"] = title + + doc = await metadata_client.upgrade_doc_to_doc_details( + doc, **(query_kwargs | kwargs) + ) + texts = read_doc(path, doc, chunk_chars=chunk_chars, overlap=100) # loose check to see if document was loaded if ( diff --git a/paperqa/prompts.py b/paperqa/prompts.py index e55e8695..3782ce17 100644 --- a/paperqa/prompts.py +++ b/paperqa/prompts.py @@ -53,6 +53,14 @@ "Citation:" ) +structured_citation_prompt = ( + "Extract the title, authors, and doi as a JSON from this MLA citation. " + "If any field can not be found, return it as null. " + "Use title, authors, and doi as keys, author's value should be a list of authors. " + "{citation}\n\n" + "Citation JSON:" +) + default_system_prompt = ( "Answer in a direct and concise tone. " "Your audience is an expert, so be highly specific. " diff --git a/paperqa/types.py b/paperqa/types.py index bdc1a721..b0ef0489 100644 --- a/paperqa/types.py +++ b/paperqa/types.py @@ -1,10 +1,14 @@ from __future__ import annotations +import logging +import re from datetime import datetime -from typing import Any, Callable +from typing import Any, Callable, ClassVar, Collection from uuid import UUID, uuid4 import tiktoken +from pybtex.database import BibliographyData, Entry, Person +from pybtex.database.input.bibtex import Parser from pydantic import ( BaseModel, ConfigDict, @@ -19,17 +23,25 @@ default_system_prompt, qa_prompt, select_paper_prompt, + structured_citation_prompt, summary_json_prompt, summary_json_system_prompt, summary_prompt, ) -from .utils import get_citenames +from .utils import ( + create_bibtex_key, + encode_id, + format_bibtex, + get_citenames, +) from .version import __version__ as pqa_version # Just for clarity DocKey = Any CallbackFactory = Callable[[str], list[Callable[[str], None]] | None] +logger = logging.getLogger(__name__) + class LLMResult(BaseModel): """A class to hold the result of a LLM completion.""" @@ -65,6 +77,10 @@ class Doc(Embeddable): docname: str citation: str dockey: DocKey + overwrite_fields_from_metadata: bool = Field( + default=True, + description="flag to overwrite fields from metadata when upgrading to a DocDetails", + ) def __hash__(self) -> int: return hash((self.docname, self.dockey)) @@ -98,6 +114,7 @@ class PromptCollection(BaseModel): qa: str = qa_prompt select: str = select_paper_prompt cite: str = citation_prompt + structured_cite: str = structured_citation_prompt pre: str | None = Field( default=None, description=( @@ -286,3 +303,370 @@ def encode_content(self): raise NotImplementedError( "Encoding only implemented for str and list[str] content." ) + + +# We use these integer values +# as defined in https://jfp.csc.fi/en/web/haku/kayttoohje +# which is a recommended ranking system +SOURCE_QUALITY_MESSAGES = { + 0: "poor quality or predatory journal", + 1: "peer-reviewed journal", + 2: "domain leading peer-reviewed journal", + 3: "highest quality peer-reviewed journal", +} + +CITATION_FALLBACK_DATA = { + "authors": ["Unknown authors"], + "author": "Unknown author(s)", + "year": "Unknown year", + "title": "Unknown title", + "journal": "Unknown journal", +} + + +class DocDetails(Doc): + model_config = ConfigDict(validate_assignment=True) + + citation: str + key: str | None = None + bibtex: str | None = None + authors: list[str] | None = None + publication_date: datetime | None = None + year: int | None = None + volume: str | None = None + issue: str | None = None # TODO: in bibtex this may be "number" + issn: str | None = None + pages: str | None = None + journal: str | None = None + publisher: str | None = None + url: str | None = Field( + default=None, + description=( + "Optional URL to the paper, which can lead to a Semantic Scholar page," + " arXiv abstract, etc. As of version 0.67 on 5/10/2024, we don't use this" + " URL anywhere in the source code." + ), + ) + title: str | None = None + citation_count: int | None = None + bibtex_type: str | None = None + + source_quality: int | None = Field( + default=None, + description="Quality of journal/venue of paper. " + " We use None as a sentinel for unset values (like for determining hydration) " + " So, we use -1 means unknown quality and None means it needs to be hydrated.", + ) + doi: str | None = None + doi_url: str | None = None + doc_id: str | None = None + other: dict[str, Any] = Field( + default_factory=dict, + description="Other metadata besides the above standardized fields.", + ) + UNDEFINED_JOURNAL_QUALITY: ClassVar[int] = -1 + + @field_validator("key") + @classmethod + def clean_key(cls, value: str) -> str: + # Replace HTML tags with empty string + return re.sub(pattern=r"<\/?\w{1,10}>", repl="", string=value) + + @staticmethod + def lowercase_doi_and_populate_doc_id(data: dict[str, Any]) -> dict[str, Any]: + if doi := data.get("doi"): + data["doi"] = doi.lower() + data["doc_id"] = encode_id(doi.lower()) + else: + data["doc_id"] = encode_id(uuid4()) + + if data.get("overwrite_fields_from_metadata", True): + data["dockey"] = data["doc_id"] + + return data + + @staticmethod + def is_bibtex_complete(bibtex: str, fields: list[str] | None = None) -> bool: + """Validate bibtex entries have certain fields.""" + if fields is None: + fields = ["doi", "title"] + return all(field + "=" in bibtex for field in fields) + + @staticmethod + def merge_bibtex_entries(entry1: Entry, entry2: Entry) -> Entry: + """Merge two bibtex entries into one, preferring entry2 fields.""" + merged_entry = Entry(entry1.type) + + for field, value in entry1.fields.items(): + merged_entry.fields[field] = value + for field, value in entry2.fields.items(): + merged_entry.fields[field] = value + + return merged_entry + + @staticmethod + def misc_string_cleaning(data: dict[str, Any]) -> dict[str, Any]: + """Clean strings before the enter the validation process.""" + if pages := data.get("pages"): + data["pages"] = pages.replace("--", "-").replace(" ", "") + return data + + @staticmethod + def inject_clean_doi_url_into_data(data: dict[str, Any]) -> dict[str, Any]: + """Ensure doi_url is present in data (since non-default arguments are not included).""" + doi_url, doi = data.get("doi_url"), data.get("doi") + + if doi and not doi_url: + doi_url = "https://doi.org/" + doi + + if doi_url: + data["doi_url"] = doi_url.replace( + "http://dx.doi.org/", "https://doi.org/" + ).lower() + + return data + + @staticmethod + def overwrite_docname_dockey_for_compatibility_w_doc( + data: dict[str, Any] + ) -> dict[str, Any]: + """Overwrite fields from metadata if specified.""" + overwrite_fields = {"key": "docname", "doc_id": "dockey"} + if data.get("overwrite_fields_from_metadata", True): + for field, old_field in overwrite_fields.items(): + if data.get(field): + data[old_field] = data[field] + return data + + @classmethod + def populate_bibtex_key_citation( # noqa: C901, PLR0912 + cls, data: dict[str, Any] + ) -> dict[str, Any]: + """Add or modify bibtex, key, and citation fields. + + Missing values, 'unknown' keys, and incomplete bibtex entries are regenerated. + + When overwrite_fields_from_metadata: + If bibtex is regenerated, the citation field is also regenerated. + + Otherwise we keep the citation field as is. + + """ + # we try to regenerate the key if unknowns are present, maybe they have been found + if not data.get("key") or "unknown" in data["key"].lower(): + data["key"] = create_bibtex_key( + data.get("authors") or CITATION_FALLBACK_DATA["authors"], # type: ignore[arg-type] + data.get("year") or CITATION_FALLBACK_DATA["year"], # type: ignore[arg-type] + data.get("title") or CITATION_FALLBACK_DATA["title"], # type: ignore[arg-type] + ) + if data.get("overwrite_fields_from_metadata", True): + data["docname"] = data["key"] + + # even if we have a bibtex, it may not be complete, thus we need to add to it + if not data.get("bibtex") or not cls.is_bibtex_complete(data["bibtex"]): + existing_entry = None + # if our bibtex already exists, but is incomplete, we add self_generated to metadata + if data.get("bibtex"): + if data.get("other"): + if ( + "bibtex_source" in data["other"] + and "self_generated" not in data["other"]["bibtex_source"] + ): + data["other"]["bibtex_source"].append("self_generated") + else: + data["other"]["bibtex_source"] = ["self_generated"] + else: + data["other"] = {"bibtex_source": ["self_generated"]} + + existing_entry = next( + iter(Parser().parse_string(data["bibtex"]).entries.values()) + ) + + entry_data = { + "title": data.get("title") or CITATION_FALLBACK_DATA["title"], + "year": ( + CITATION_FALLBACK_DATA["year"] + if not data.get("year") + else str(data["year"]) + ), + "journal": data.get("journal") or CITATION_FALLBACK_DATA["journal"], + "volume": data.get("volume"), + "pages": data.get("pages"), + "month": ( + None + if not data.get("publication_date") + else data["publication_date"].strftime("%b") + ), + "doi": data.get("doi"), + "url": data.get("doi_url"), + "publisher": data.get("publisher"), + "issue": data.get("issue"), + "issn": data.get("issn"), + } + entry_data = {k: v for k, v in entry_data.items() if v} + try: + new_entry = Entry(data.get("bibtex_type", "article"), fields=entry_data) + if existing_entry: + new_entry = cls.merge_bibtex_entries(existing_entry, new_entry) + # add in authors manually into the entry + authors = [Person(a) for a in data.get("authors", ["Unknown authors"])] + for a in authors: + new_entry.add_person(a, "author") + data["bibtex"] = BibliographyData( + entries={data["key"]: new_entry} + ).to_string("bibtex") + # clear out the citation, since it will be regenerated + if data.get("overwrite_fields_from_metadata", True): + data["citation"] = None + except Exception: + logger.exception(f"Failed to generate bibtex for {data}") + if not data.get("citation"): + data["citation"] = format_bibtex( + data["bibtex"], clean=True, missing_replacements=CITATION_FALLBACK_DATA # type: ignore[arg-type] + ) + return data + + @model_validator(mode="before") + @classmethod + def validate_all_fields(cls, data: dict[str, Any]) -> dict[str, Any]: + data = cls.lowercase_doi_and_populate_doc_id(data) + data = cls.misc_string_cleaning(data) + data = cls.inject_clean_doi_url_into_data(data) + data = cls.populate_bibtex_key_citation(data) + return cls.overwrite_docname_dockey_for_compatibility_w_doc(data) + + def __getitem__(self, item: str): + """Allow for dictionary-like access, falling back on other.""" + try: + return getattr(self, item) + except AttributeError: + return self.other[item] + + @property + def formatted_citation(self) -> str: + if ( + self.citation is None # type: ignore[redundant-expr] + or self.citation_count is None + or self.source_quality is None + ): + raise ValueError( + "Citation, citationCount, and sourceQuality are not set -- do you need to call `hydrate`?" + ) + quality = ( + SOURCE_QUALITY_MESSAGES[self.source_quality] + if self.source_quality >= 0 + else None + ) + if quality is None: + return f"{self.citation} This article has {self.citation_count} citations." + return ( + f"{self.citation} This article has {self.citation_count} citations and is from a " + f"{quality}." + ) + + OPTIONAL_HYDRATION_FIELDS: ClassVar[Collection[str]] = {"url"} + + def is_hydration_needed( # pylint: disable=dangerous-default-value + self, + exclusion: Collection[str] = OPTIONAL_HYDRATION_FIELDS, + inclusion: Collection[str] = [], + ) -> bool: + """Determine if we have unfilled attributes.""" + if inclusion: + return any( + v is None for k, v in self.model_dump().items() if k in inclusion + ) + return any( + v is None for k, v in self.model_dump().items() if k not in exclusion + ) + + def repopulate_doc_id_from_doi(self) -> None: + # TODO: should this be a hash of the doi? + if self.doi: + self.doc_id = encode_id(self.doi) + + def __add__(self, other: DocDetails | int) -> DocDetails: # noqa: C901 + """Merge two DocDetails objects together.""" + # control for usage w. Python's sum() function + if isinstance(other, int): + return self + + # first see if one of the entries is newer, which we will prefer + PREFER_OTHER = True + if self.publication_date and other.publication_date: + PREFER_OTHER = self.publication_date <= other.publication_date + + merged_data = {} + for field in self.model_fields: + self_value = getattr(self, field) + other_value = getattr(other, field) + + if field == "other": + # Merge 'other' dictionaries + merged_data[field] = {**self.other, **other.other} + # handle the bibtex / sources as special fields + for field_to_combine in ["bibtex_source", "client_source"]: + if self.other.get(field_to_combine) and other.other.get( + field_to_combine + ): + # Note: these should always be lists + merged_data[field][field_to_combine] = ( + self.other[field_to_combine] + other.other[field_to_combine] + ) + + elif field == "authors" and self_value and other_value: + # Combine authors lists, removing duplicates + # Choose whichever author list is longer + best_authors = ( + self.authors + if ( + sum(len(a) for a in (self.authors or [])) + >= sum(len(a) for a in (other.authors or [])) + ) + else other.authors + ) + merged_data[field] = best_authors or None # type: ignore[assignment] + + elif field == "key" and self_value is not None and other_value is not None: + # if we have multiple keys, we wipe them and allow regeneration + merged_data[field] = None # type: ignore[assignment] + + elif ( + field in {"citation_count", "year", "publication_date"} + and self_value is not None + and other_value is not None + ): + # get the latest data + merged_data[field] = max(self_value, other_value) + + else: + # Prefer non-null values, default preference for 'other' object. + # Note: if PREFER_OTHER = False then even if 'other' data exists + # we will use 'self' data. This is to control for when we have + # pre-prints / arXiv versions of papers that are not as up-to-date + merged_data[field] = ( + other_value + if (other_value is not None and PREFER_OTHER) + else self_value + ) + + # Recalculate doc_id if doi has changed + if merged_data["doi"] != self.doi: + merged_data["doc_id"] = ( + encode_id(merged_data["doi"].lower()) if merged_data["doi"] else None # type: ignore[attr-defined,assignment] + ) + + # Create and return new DocDetails instance + return DocDetails(**merged_data) + + def __radd__(self, other: DocDetails | int) -> DocDetails: + # other == 0 captures the first call of sum() + if isinstance(other, int) and other == 0: + return self + return self.__add__(other) + + def __iadd__(self, other: DocDetails | int) -> DocDetails: # noqa: PYI034 + # only includes int to align with __radd__ and __add__ + if isinstance(other, int): + return self + return self.__add__(other) diff --git a/paperqa/utils.py b/paperqa/utils.py index f75ab128..19f521e0 100644 --- a/paperqa/utils.py +++ b/paperqa/utils.py @@ -1,15 +1,38 @@ from __future__ import annotations import asyncio +import hashlib import inspect import json +import logging import math import re import string +from collections.abc import Iterable +from datetime import datetime +from functools import reduce +from http import HTTPStatus from pathlib import Path -from typing import Any, BinaryIO, Coroutine, Iterator, Union +from typing import Any, BinaryIO, Collection, Coroutine, Iterator, Union +from uuid import UUID +import aiohttp +import httpx import pypdf +from pybtex.database import Person, parse_string +from pybtex.database.input.bibtex import Parser +from pybtex.style.formatting import unsrtalpha +from pybtex.style.template import FieldIsMissing +from tenacity import ( + before_sleep_log, + retry, + retry_if_exception, + stop_after_attempt, + wait_incrementing, +) + +logger = logging.getLogger(__name__) + StrPath = Union[str, Path] @@ -192,3 +215,207 @@ def replace_newlines(match: re.Match) -> str: text = re.sub(pattern, replace_newlines, text) return json.loads(text) + + +def encode_id(value: str | bytes | UUID, maxsize: int | None = 16) -> str: + """Encode a value (e.g. a DOI) optionally with a max length.""" + if isinstance(value, UUID): + value = str(value) + if isinstance(value, str): + value = value.lower().encode() + return hashlib.md5(value).hexdigest()[:maxsize] # noqa: S324 + + +def get_year(ts: datetime | None = None) -> str: + """Get the year from the input datetime, otherwise using the current datetime.""" + if ts is None: + ts = datetime.now() + return ts.strftime("%Y") + + +class CitationConversionError(Exception): + """Exception to throw when we can't process a citation from a BibTeX.""" + + +def clean_upbibtex(bibtex: str) -> str: + + if not bibtex: + return bibtex + + mapping = { + "None": "article", + "Article": "article", + "JournalArticle": "article", + "Review": "article", + "Book": "book", + "BookSection": "inbook", + "ConferencePaper": "inproceedings", + "Conference": "inproceedings", + "Dataset": "misc", + "Dissertation": "phdthesis", + "Journal": "article", + "Patent": "patent", + "Preprint": "article", + "Report": "techreport", + "Thesis": "phdthesis", + "WebPage": "misc", + "Plain": "article", + } + if "@None" in bibtex: + return bibtex.replace("@None", "@article") + match = re.findall(r"@\['(.*)'\]", bibtex) + if not match: + match = re.findall(r"@(\w+)\{", bibtex) + bib_type = match[0] + current = f"@{match[0]}" + else: + bib_type = match[0] + current = f"@['{bib_type}']" + for k, v in mapping.items(): + # can have multiple + if k in bib_type: + bibtex = bibtex.replace(current, f"@{v}") + break + return bibtex + + +def format_bibtex( # noqa: C901 + bibtex: str, + key: str | None = None, + clean: bool = True, + missing_replacements: dict[str, str] | None = None, +) -> str: + """Transform bibtex entry into a citation, potentially adding missing fields.""" + if missing_replacements is None: + missing_replacements = {} + if key is None: + key = bibtex.split("{")[1].split(",")[0] + style = unsrtalpha.Style() + try: + bd = parse_string(clean_upbibtex(bibtex) if clean else bibtex, "bibtex") + except Exception: + return "Ref " + key + try: + entry = bd.entries[key] + except KeyError as exc: # Let's check if key is a non-empty prefix + try: + entry = next( + iter(v for k, v in bd.entries.items() if k.startswith(key) and key) + ) + except StopIteration: + raise CitationConversionError( + f"Failed to process{' and clean up' if clean else ''} bibtex {bibtex}" + f" due to failed lookup of key {key}." + ) from exc + try: + # see if we can insert missing fields + for field, replacement_value in missing_replacements.items(): + # Deal with special case for author, since it needs to be parsed + # into Person objects. This reorganizes the names automatically. + if field == "author" and "author" not in entry.persons: + tmp_author_bibtex = f"@misc{{tmpkey, author={{{replacement_value}}}}}" + authors: list[Person] = ( + Parser() + .parse_string(tmp_author_bibtex) + .entries["tmpkey"] + .persons["author"] + ) + for a in authors: + entry.add_person(a, "author") + elif field not in entry.fields: + entry.fields.update({field: replacement_value}) + entry = style.format_entry(label="1", entry=entry) + return entry.text.render_as("text") + except (FieldIsMissing, UnicodeDecodeError): + try: + return entry.fields["title"] + except KeyError as exc: + raise CitationConversionError( + f"Failed to process{' and clean up' if clean else ''} bibtex {bibtex}" + " due to missing a 'title' field." + ) from exc + + +def remove_substrings(target: str, substr_removal_list: Collection[str]) -> str: + """Remove substrings from a target string.""" + if all(len(w) == 1 for w in substr_removal_list): + return target.translate(str.maketrans("", "", "".join(substr_removal_list))) + + for substr in substr_removal_list: + target = target.replace(substr, "") + return target + + +def bibtex_field_extract( + bibtex: str, field: str, missing_replacements: dict[str, str] | None = None +) -> str: + """Get a field from a bibtex entry. + + Args: + bibtex: bibtex entry + field: field to extract + missing_replacements: replacement extract for field if not present in the bibtex string + """ + if missing_replacements is None: + missing_replacements = {} + try: + pattern = rf"{field}\s*=\s*{{(.*?)}}," + # note: we intentionally have an attribute error if no match + return re.search(pattern, bibtex, re.IGNORECASE).group(1).strip() # type: ignore[union-attr] + except AttributeError: + return missing_replacements.get(field, "") + + +def create_bibtex_key(author: list[str], year: str, title: str) -> str: + FORBIDDEN_KEY_CHARACTERS = {"_", " ", "-", "/", "'", "`", ":"} + author_rep = ( + author[0].split()[-1].casefold() + if "Unknown" not in author[0] + else "unknownauthors" + ) + key = ( + f"{author_rep}{year}{''.join([t.casefold() for t in title.split()[:3]])[:100]}" + ) + return remove_substrings(key, FORBIDDEN_KEY_CHARACTERS) + + +@retry( + retry=retry_if_exception( + lambda x: isinstance(x, aiohttp.ServerDisconnectedError) + or isinstance(x, aiohttp.ClientResponseError) + and x.status + in { + httpx.codes.INTERNAL_SERVER_ERROR.value, + httpx.codes.GATEWAY_TIMEOUT.value, + } + ), + before_sleep=before_sleep_log(logger, logging.WARNING), + stop=stop_after_attempt(5), + wait=wait_incrementing(0.1, 0.1), +) +async def _get_with_retrying( + url: str, + params: dict[str, Any], + session: aiohttp.ClientSession, + headers: dict[str, str] | None = None, + timeout: float = 10.0, + http_exception_mappings: dict[HTTPStatus | int, Exception] | None = None, +) -> dict[str, Any]: + """Get from a URL with retrying protection.""" + try: + async with session.get( + url, + params=params, + headers=headers, + timeout=aiohttp.ClientTimeout(timeout), + ) as response: + response.raise_for_status() + return await response.json() + except aiohttp.ClientResponseError as e: + if http_exception_mappings and e.status in http_exception_mappings: + raise http_exception_mappings[e.status] from e + raise + + +def union_collections_to_ordered_list(collections: Iterable) -> list: + return sorted(reduce(lambda x, y: set(x) | set(y), collections)) diff --git a/pyproject.toml b/pyproject.toml index 95f436ce..b8e5bbd6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,6 +23,7 @@ dependencies = [ "html2text", "numpy", "openai>=1", + "pybtex", "pydantic~=2.0", "pypdf", "tiktoken>=0.4.0", diff --git a/tests/.gitignore b/tests/.gitignore new file mode 100644 index 00000000..a8d8e0c7 --- /dev/null +++ b/tests/.gitignore @@ -0,0 +1,3 @@ +# ignore test-generated files +example.* +example2.* diff --git a/tests/cassettes/test_author_matching.yaml b/tests/cassettes/test_author_matching.yaml new file mode 100644 index 00000000..cedcb2d6 --- /dev/null +++ b/tests/cassettes/test_author_matching.yaml @@ -0,0 +1,195 @@ +interactions: + - request: + body: null + headers: {} + method: GET + uri: https://api.crossref.org/works?mailto=test@example.com&query.title=Augmenting+large+language+models+with+chemistry+tools&rows=1&query.author=Jack+NoScience&select=DOI,author,title + response: + body: + string: + '{"status":"ok","message-type":"work-list","message-version":"1.0.0","message":{"facets":{},"total-results":3960,"items":[{"DOI":"10.4337\/cilj.2023.02.08","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-2467-681X","authenticated-orcid":true,"given":"Jack + Wright","family":"Nelson","sequence":"first","affiliation":[{"name":"Doctoral + Candidate, McGill University Faculty of Law, Montreal, QC, Canada"},{"name":"Adjunct + Research Fellow, National University of Singapore Faculty of Law, Singapore"}]}],"title":["Large + language models and the treaty interpretation game"]}],"items-per-page":1,"query":{"start-index":0,"search-terms":null}}}' + headers: + Access-Control-Allow-Headers: + - X-Requested-With, Accept, Accept-Encoding, Accept-Charset, Accept-Language, + Accept-Ranges, Cache-Control + Access-Control-Allow-Origin: + - 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X-Requested-With, Accept, Accept-Encoding, Accept-Charset, Accept-Language, + Accept-Ranges, Cache-Control + Access-Control-Allow-Origin: + - "*" + Access-Control-Expose-Headers: + - Link + Connection: + - close + Content-Type: + - application/json + Date: + - Tue, 13 Aug 2024 18:34:05 GMT + Server: + - Jetty(9.4.40.v20210413) + Transfer-Encoding: + - chunked + permissions-policy: + - interest-cohort=() + x-api-pool: + - plus + x-rate-limit-interval: + - 1s + x-rate-limit-limit: + - "150" + x-ratelimit-interval: + - 1s + x-ratelimit-limit: + - "150" + status: + code: 200 + message: OK + - request: + body: null + headers: {} + method: GET + uri: https://api.semanticscholar.org/graph/v1/paper/search/match?query=askldjrq3rjaw938h&fields=authors,citationCount,citationStyles,externalIds,influentialCitationCount,isOpenAccess,journal,openAccessPdf,publicationDate,publicationTypes,title,url,venue,year + response: + body: + string: '{"error":"Title match not found"} + + ' + headers: + Access-Control-Allow-Origin: + - "*" + Connection: + - keep-alive + Content-Length: + - "34" + Content-Type: + - application/json + Date: + - Tue, 13 Aug 2024 18:34:07 GMT + Via: + - 1.1 b3169f8fae0104e39a0a9728b6537e08.cloudfront.net (CloudFront) + X-Amz-Cf-Id: + - njac2dCY2mYDBr9kpqMw07vocYKj5bqWdB3gjSS35BKQnXDemHVPdw== + X-Amz-Cf-Pop: + - IAD55-P4 + X-Cache: + - Error from cloudfront + x-amz-apigw-id: + - cdcMuFLwPHcEjHQ= + x-amzn-Remapped-Connection: + - keep-alive + x-amzn-Remapped-Content-Length: + - "34" + x-amzn-Remapped-Date: + - Tue, 13 Aug 2024 18:34:07 GMT + x-amzn-Remapped-Server: + - gunicorn + x-amzn-RequestId: + - c9ee1896-0b67-4677-b6ed-dd3c7c274fd1 + status: + code: 404 + message: Not Found + - request: + body: null + headers: {} + method: GET + uri: https://api.crossref.org/works?mailto=test@example.com&query.title=Effect+of+native+oxide+layers+on+copper+thin-film+tensile+properties:+A+study&rows=1 + response: + body: + string: + '{"status":"ok","message-type":"work-list","message-version":"1.0.0","message":{"facets":{},"total-results":10275318,"items":[{"indexed":{"date-parts":[[2023,9,29]],"date-time":"2023-09-29T22:47:50Z","timestamp":1696027670718},"reference-count":57,"publisher":"AIP + Publishing","issue":"23","funder":[{"DOI":"10.13039\/100000006","name":"Office + of Naval Research","doi-asserted-by":"publisher","award":["N00014-12-1-0542"]}],"content-domain":{"domain":["pubs.aip.org"],"crossmark-restriction":true},"published-print":{"date-parts":[[2015,12,21]]},"abstract":"Metal-oxide + layers are likely to be present on metallic nano-structures due to either + environmental exposure during use, or high temperature processing techniques + such as annealing. It is well known that nano-structured metals have vastly + different mechanical properties from bulk metals; however, difficulties in + modeling the transition between metallic and ionic bonding have prevented + the computational investigation of the effects of oxide surface layers. Newly + developed charge-optimized many body [Liang et al., Mater. Sci. Eng., R 74, + 255 (2013)] potentials are used to perform fully reactive molecular dynamics + simulations which elucidate the effects that metal-oxide layers have on the + mechanical properties of a copper thin-film. Simulated tensile tests are performed + on thin-films while using different strain-rates, temperatures, and oxide + thicknesses to evaluate changes in yield stress, modulus, and failure mechanisms. + Findings indicate that copper-thin film mechanical properties are strongly + affected by native oxide layers. The formed oxide layers have an amorphous + structure with lower Cu-O bond-densities than bulk CuO, and a mixture of Cu2O + and CuO charge character. It is found that oxidation will cause modifications + to the strain response of the elastic modulii, producing a stiffened modulii + at low temperatures (&lt;75\u2009K) and low strain values (&lt;5%), + and a softened modulii at higher temperatures. While under strain, structural + reorganization within the oxide layers facilitates brittle yielding through + nucleation of defects across the oxide\/metal interface. The oxide-free copper + thin-film yielding mechanism is found to be a tensile-axis reorientation and + grain creation. The oxide layers change the observed yielding mechanism, allowing + for the inner copper thin-film to sustain an FCC-to-BCC transition during + yielding. The mechanical properties are fit to a thermodynamic model based + on classical nucleation theory. 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While multiplexed assays of variant effect (MAVEs) have + enabled scalable functional assessment of variants, established MAVEs are + limited by either exogenous expression of variants or constraints of genome + editing. Here, we introduce a pooled prime editing (PE) platform in haploid + human cells to scalably assay variants in their endogenous context. We first + optimized delivery of variants to HAP1 cells, defining optimal pegRNA designs + and establishing a co-selection strategy for improved efficiency. We characterize + our platform in the context of negative selection by testing over 7,500 pegRNAs + targetingSMARCB1<\/jats:italic>for editing activity and observing + depletion of highly active pegRNAs installing loss-of-function variants. We + next assess variants inMLH1<\/jats:italic>via 6-thioguanine selection, + assaying 65.3% of all possible SNVs in a 200-bp region spanning exon 10 and + distinguishing LoF variants with high accuracy. Lastly, we assay 362 non-codingMLH1<\/jats:italic>variants + across a 60 kb region in a single experiment, identifying pathogenic variants + acting via multiple mechanisms with high specificity. Our analyses detail + how filtering for highly active pegRNAs can facilitate both positive and negative + selection screens. Accordingly, our platform promises to enable highly scalable + functional assessment of human variants.<\/jats:p>","DOI":"10.1101\/2024.04.01.587366","type":"posted-content","created":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T02:05:17Z","timestamp":1712023517000},"source":"Crossref","is-referenced-by-count":0,"title":["High-throughput + screening of human genetic variants by pooled prime editing"],"prefix":"10.1101","author":[{"given":"Michael","family":"Herger","sequence":"first","affiliation":[]},{"given":"Christina + M.","family":"Kajba","sequence":"additional","affiliation":[]},{"given":"Megan","family":"Buckley","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Cunha","sequence":"additional","affiliation":[]},{"given":"Molly","family":"Strom","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-7767-8608","authenticated-orcid":false,"given":"Gregory + M.","family":"Findlay","sequence":"additional","affiliation":[]}],"member":"246","reference":[{"key":"2024040415500652000_2024.04.01.587366v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2015.30"},{"key":"2024040415500652000_2024.04.01.587366v1.2","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.cels.2017.11.003","article-title":"Quantitative + Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data","volume":"6","year":"2018","journal-title":"Cell + Syst"},{"key":"2024040415500652000_2024.04.01.587366v1.3","doi-asserted-by":"publisher","DOI":"10.1126\/science.abi8207"},{"key":"2024040415500652000_2024.04.01.587366v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2018.12.015"},{"key":"2024040415500652000_2024.04.01.587366v1.5","doi-asserted-by":"crossref","first-page":"eabn8153","DOI":"10.1126\/science.abn8197","article-title":"The + landscape of tolerated genetic variation in humans and primates","volume":"380","year":"2023","journal-title":"Science"},{"key":"2024040415500652000_2024.04.01.587366v1.6","doi-asserted-by":"crossref","first-page":"eadg7492","DOI":"10.1126\/science.adg7492","article-title":"Accurate + proteome-wide missense variant effect prediction with AlphaMissense","volume":"381","year":"2023","journal-title":"Science"},{"key":"2024040415500652000_2024.04.01.587366v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1222"},{"key":"2024040415500652000_2024.04.01.587366v1.8","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1038\/s41436-021-01172-3","article-title":"ACMG + SF v3.0 list for reporting of secondary findings in clinical exome and genome + sequencing: a policy statement of the American College of Medical Genetics + and Genomics (ACMG)","volume":"23","year":"2021","journal-title":"Genet. 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It is well known that nano-structured metals have vastly + different mechanical properties from bulk metals; however, difficulties in + modeling the transition between metallic and ionic bonding have prevented + the computational investigation of the effects of oxide surface layers. Newly + developed charge-optimized many body [Liang et al., Mater. Sci. Eng., R 74, + 255 (2013)] potentials are used to perform fully reactive molecular dynamics + simulations which elucidate the effects that metal-oxide layers have on the + mechanical properties of a copper thin-film. Simulated tensile tests are performed + on thin-films while using different strain-rates, temperatures, and oxide + thicknesses to evaluate changes in yield stress, modulus, and failure mechanisms. + Findings indicate that copper-thin film mechanical properties are strongly + affected by native oxide layers. The formed oxide layers have an amorphous + structure with lower Cu-O bond-densities than bulk CuO, and a mixture of Cu2O + and CuO charge character. It is found that oxidation will cause modifications + to the strain response of the elastic modulii, producing a stiffened modulii + at low temperatures (&lt;75\u2009K) and low strain values (&lt;5%), + and a softened modulii at higher temperatures. While under strain, structural + reorganization within the oxide layers facilitates brittle yielding through + nucleation of defects across the oxide\/metal interface. The oxide-free copper + thin-film yielding mechanism is found to be a tensile-axis reorientation and + grain creation. The oxide layers change the observed yielding mechanism, allowing + for the inner copper thin-film to sustain an FCC-to-BCC transition during + yielding. The mechanical properties are fit to a thermodynamic model based + on classical nucleation theory. The fit implies that the oxidation of the + films reduces the activation volume for yielding.<\/jats:p>","DOI":"10.1063\/1.4938384","type":"journal-article","created":{"date-parts":[[2015,12,22]],"date-time":"2015-12-22T00:59:18Z","timestamp":1450745958000},"update-policy":"http:\/\/dx.doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":8,"title":["Effect + of native oxide layers on copper thin-film tensile properties: A reactive + molecular dynamics study"],"prefix":"10.1063","volume":"118","author":[{"given":"Michael + D.","family":"Skarlinski","sequence":"first","affiliation":[{"name":"University + of Rochester 1 Materials Science Program, , Rochester, New York 14627, USA"}]},{"given":"David + J.","family":"Quesnel","sequence":"additional","affiliation":[{"name":"University + of Rochester 1 Materials Science Program, , Rochester, New York 14627, USA"},{"name":"University + of Rochester 2 Department of Mechanical Engineering, , Rochester, New York + 14627, USA"}]}],"member":"317","published-online":{"date-parts":[[2015,12,21]]},"reference":[{"key":"2023062402360541600_c1","doi-asserted-by":"publisher","first-page":"10973","DOI":"10.1021\/nn504883m","volume":"8","year":"2014","journal-title":"ACS + Nano"},{"key":"2023062402360541600_c2","volume-title":"Ultrathin Metal Transparent + Electrodes for the Optoelectronics Industry","year":"2013"},{"key":"2023062402360541600_c3","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.1039\/b718768h","volume":"37","year":"2008","journal-title":"Chem. + Soc. 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We also created an ensemble of three state-of-the-art deep learning + models to classify rationale of support, refute, and neutral. We then constructed + CoVERt, a new COVID VERification dataset comprising 15 PICO-encoded drug claims + accompanied by 96 manually selected and labeled clinical trial abstracts that + either support or refute each claim. We used CoVERt and SciFact (a public + scientific claim verification dataset) to assess CliVER\u2019s performance + in predicting labels. Finally, we compared CliVER to clinicians in the verification + of 19 claims from 6 disease domains, using 189\u00a0648 PubMed abstracts extracted + from January 2010 to October 2021.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n In + the evaluation of label prediction accuracy on CoVERt, CliVER achieved a notable + F1 score of 0.92, highlighting the efficacy of the retrieval-augmented models. + The ensemble model outperforms each individual state-of-the-art model by an + absolute increase from 3% to 11% in the F1 score. Moreover, when compared + with four clinicians, CliVER achieved a precision of 79.0% for abstract retrieval, + 67.4% for sentence selection, and 63.2% for label prediction, respectively.<\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n CliVER + demonstrates its early potential to automate scientific claim verification + using retrieval-augmented strategies to harness the wealth of clinical trial + abstracts in PubMed. Future studies are warranted to further test its clinical + utility.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/jamiaopen\/ooae021","type":"journal-article","created":{"date-parts":[[2024,2,22]],"date-time":"2024-02-22T01:48:17Z","timestamp":1708566497000},"source":"Crossref","is-referenced-by-count":0,"title":["Retrieval + augmented scientific claim verification"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-1975-1272","authenticated-orcid":false,"given":"Hao","family":"Liu","sequence":"first","affiliation":[{"name":"School + of Computing, Montclair State University , Montclair, NJ 07043, United States"}]},{"given":"Ali","family":"Soroush","sequence":"additional","affiliation":[{"name":"Department + of Medicine, Columbia University , New York, NY 10027, United States"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-1418-3103","authenticated-orcid":false,"given":"Jordan + G","family":"Nestor","sequence":"additional","affiliation":[{"name":"Department + of Medicine, Columbia University , New York, NY 10027, United States"}]},{"given":"Elizabeth","family":"Park","sequence":"additional","affiliation":[{"name":"Department + of Medicine, Columbia University , New York, NY 10027, United States"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-4318-5987","authenticated-orcid":false,"given":"Betina","family":"Idnay","sequence":"additional","affiliation":[{"name":"Department + of Biomedical Informatics, Columbia University , New York, NY 10027, United + States"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-2681-1931","authenticated-orcid":false,"given":"Yilu","family":"Fang","sequence":"additional","affiliation":[{"name":"Department + of Biomedical Informatics, Columbia University , New York, NY 10027, United + States"}]},{"given":"Jane","family":"Pan","sequence":"additional","affiliation":[{"name":"Department + of Applied Physics and Applied Mathematics, Columbia University , New York, + NY 10027, United States"}]},{"given":"Stan","family":"Liao","sequence":"additional","affiliation":[{"name":"Department + of Applied Physics and Applied Mathematics, Columbia University , New York, + NY 10027, United States"}]},{"given":"Marguerite","family":"Bernard","sequence":"additional","affiliation":[{"name":"Institute + of Human Nutrition, Columbia University , New York, NY 10027, United States"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9309-8331","authenticated-orcid":false,"given":"Yifan","family":"Peng","sequence":"additional","affiliation":[{"name":"Department + of Population Health Sciences, Weill Cornell Medicine , New York, NY 10065, + United States"}]},{"given":"Chunhua","family":"Weng","sequence":"additional","affiliation":[{"name":"Department + of Biomedical Informatics, Columbia University , New York, NY 10027, United + 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While multiplexed assays of variant effect (MAVEs) have + enabled scalable functional assessment of variants, established MAVEs are + limited by either exogenous expression of variants or constraints of genome + editing. Here, we introduce a pooled prime editing (PE) platform in haploid + human cells to scalably assay variants in their endogenous context. We first + optimized delivery of variants to HAP1 cells, defining optimal pegRNA designs + and establishing a co-selection strategy for improved efficiency. We characterize + our platform in the context of negative selection by testing over 7,500 pegRNAs + targetingSMARCB1<\/jats:italic>for editing activity and observing + depletion of highly active pegRNAs installing loss-of-function variants. We + next assess variants inMLH1<\/jats:italic>via 6-thioguanine selection, + assaying 65.3% of all possible SNVs in a 200-bp region spanning exon 10 and + distinguishing LoF variants with high accuracy. Lastly, we assay 362 non-codingMLH1<\/jats:italic>variants + across a 60 kb region in a single experiment, identifying pathogenic variants + acting via multiple mechanisms with high specificity. Our analyses detail + how filtering for highly active pegRNAs can facilitate both positive and negative + selection screens. Accordingly, our platform promises to enable highly scalable + functional assessment of human variants.<\/jats:p>","DOI":"10.1101\/2024.04.01.587366","type":"posted-content","created":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T02:05:17Z","timestamp":1712023517000},"source":"Crossref","is-referenced-by-count":0,"title":["High-throughput + screening of human genetic variants by pooled prime editing"],"prefix":"10.1101","author":[{"given":"Michael","family":"Herger","sequence":"first","affiliation":[]},{"given":"Christina + M.","family":"Kajba","sequence":"additional","affiliation":[]},{"given":"Megan","family":"Buckley","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Cunha","sequence":"additional","affiliation":[]},{"given":"Molly","family":"Strom","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-7767-8608","authenticated-orcid":false,"given":"Gregory + M.","family":"Findlay","sequence":"additional","affiliation":[]}],"member":"246","reference":[{"key":"2024040415500652000_2024.04.01.587366v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2015.30"},{"key":"2024040415500652000_2024.04.01.587366v1.2","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.cels.2017.11.003","article-title":"Quantitative + Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data","volume":"6","year":"2018","journal-title":"Cell + Syst"},{"key":"2024040415500652000_2024.04.01.587366v1.3","doi-asserted-by":"publisher","DOI":"10.1126\/science.abi8207"},{"key":"2024040415500652000_2024.04.01.587366v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2018.12.015"},{"key":"2024040415500652000_2024.04.01.587366v1.5","doi-asserted-by":"crossref","first-page":"eabn8153","DOI":"10.1126\/science.abn8197","article-title":"The + landscape of tolerated genetic variation in humans and primates","volume":"380","year":"2023","journal-title":"Science"},{"key":"2024040415500652000_2024.04.01.587366v1.6","doi-asserted-by":"crossref","first-page":"eadg7492","DOI":"10.1126\/science.adg7492","article-title":"Accurate + proteome-wide missense variant effect prediction with AlphaMissense","volume":"381","year":"2023","journal-title":"Science"},{"key":"2024040415500652000_2024.04.01.587366v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1222"},{"key":"2024040415500652000_2024.04.01.587366v1.8","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1038\/s41436-021-01172-3","article-title":"ACMG + SF v3.0 list for reporting of secondary findings in clinical exome and genome + sequencing: a policy statement of the American College of Medical Genetics + and Genomics (ACMG)","volume":"23","year":"2021","journal-title":"Genet. 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It is well known that nano-structured metals have vastly + different mechanical properties from bulk metals; however, difficulties in + modeling the transition between metallic and ionic bonding have prevented + the computational investigation of the effects of oxide surface layers. Newly + developed charge-optimized many body [Liang et al., Mater. Sci. Eng., R 74, + 255 (2013)] potentials are used to perform fully reactive molecular dynamics + simulations which elucidate the effects that metal-oxide layers have on the + mechanical properties of a copper thin-film. Simulated tensile tests are performed + on thin-films while using different strain-rates, temperatures, and oxide + thicknesses to evaluate changes in yield stress, modulus, and failure mechanisms. + Findings indicate that copper-thin film mechanical properties are strongly + affected by native oxide layers. The formed oxide layers have an amorphous + structure with lower Cu-O bond-densities than bulk CuO, and a mixture of Cu2O + and CuO charge character. It is found that oxidation will cause modifications + to the strain response of the elastic modulii, producing a stiffened modulii + at low temperatures (&lt;75\u2009K) and low strain values (&lt;5%), + and a softened modulii at higher temperatures. While under strain, structural + reorganization within the oxide layers facilitates brittle yielding through + nucleation of defects across the oxide\/metal interface. The oxide-free copper + thin-film yielding mechanism is found to be a tensile-axis reorientation and + grain creation. The oxide layers change the observed yielding mechanism, allowing + for the inner copper thin-film to sustain an FCC-to-BCC transition during + yielding. The mechanical properties are fit to a thermodynamic model based + on classical nucleation theory. 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While multiplexed assays of variant effect (MAVEs) have + enabled scalable functional assessment of variants, established MAVEs are + limited by either exogenous expression of variants or constraints of genome + editing. Here, we introduce a pooled prime editing (PE) platform in haploid + human cells to scalably assay variants in their endogenous context. We first + optimized delivery of variants to HAP1 cells, defining optimal pegRNA designs + and establishing a co-selection strategy for improved efficiency. We characterize + our platform in the context of negative selection by testing over 7,500 pegRNAs + targetingSMARCB1<\/jats:italic>for editing activity and observing + depletion of highly active pegRNAs installing loss-of-function variants. We + next assess variants inMLH1<\/jats:italic>via 6-thioguanine selection, + assaying 65.3% of all possible SNVs in a 200-bp region spanning exon 10 and + distinguishing LoF variants with high accuracy. Lastly, we assay 362 non-codingMLH1<\/jats:italic>variants + across a 60 kb region in a single experiment, identifying pathogenic variants + acting via multiple mechanisms with high specificity. Our analyses detail + how filtering for highly active pegRNAs can facilitate both positive and negative + selection screens. 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It is well known that nano-structured metals have vastly + different mechanical properties from bulk metals; however, difficulties in + modeling the transition between metallic and ionic bonding have prevented + the computational investigation of the effects of oxide surface layers. Newly + developed charge-optimized many body [Liang et al., Mater. Sci. Eng., R 74, + 255 (2013)] potentials are used to perform fully reactive molecular dynamics + simulations which elucidate the effects that metal-oxide layers have on the + mechanical properties of a copper thin-film. Simulated tensile tests are performed + on thin-films while using different strain-rates, temperatures, and oxide + thicknesses to evaluate changes in yield stress, modulus, and failure mechanisms. + Findings indicate that copper-thin film mechanical properties are strongly + affected by native oxide layers. The formed oxide layers have an amorphous + structure with lower Cu-O bond-densities than bulk CuO, and a mixture of Cu2O + and CuO charge character. It is found that oxidation will cause modifications + to the strain response of the elastic modulii, producing a stiffened modulii + at low temperatures (&lt;75\u2009K) and low strain values (&lt;5%), + and a softened modulii at higher temperatures. While under strain, structural + reorganization within the oxide layers facilitates brittle yielding through + nucleation of defects across the oxide\/metal interface. The oxide-free copper + thin-film yielding mechanism is found to be a tensile-axis reorientation and + grain creation. The oxide layers change the observed yielding mechanism, allowing + for the inner copper thin-film to sustain an FCC-to-BCC transition during + yielding. The mechanical properties are fit to a thermodynamic model based + on classical nucleation theory. 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We also created an ensemble of three state-of-the-art deep learning + models to classify rationale of support, refute, and neutral. We then constructed + CoVERt, a new COVID VERification dataset comprising 15 PICO-encoded drug claims + accompanied by 96 manually selected and labeled clinical trial abstracts that + either support or refute each claim. We used CoVERt and SciFact (a public + scientific claim verification dataset) to assess CliVER\u2019s performance + in predicting labels. Finally, we compared CliVER to clinicians in the verification + of 19 claims from 6 disease domains, using 189\u00a0648 PubMed abstracts extracted + from January 2010 to October 2021.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n In + the evaluation of label prediction accuracy on CoVERt, CliVER achieved a notable + F1 score of 0.92, highlighting the efficacy of the retrieval-augmented models. + The ensemble model outperforms each individual state-of-the-art model by an + absolute increase from 3% to 11% in the F1 score. Moreover, when compared + with four clinicians, CliVER achieved a precision of 79.0% for abstract retrieval, + 67.4% for sentence selection, and 63.2% for label prediction, respectively.<\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n CliVER + demonstrates its early potential to automate scientific claim verification + using retrieval-augmented strategies to harness the wealth of clinical trial + abstracts in PubMed. 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Skarlinski", "David J. Quesnel"], + "formatted_citation": ( + "Michael D. Skarlinski and David J. Quesnel. Effect of native " + "oxide layers on copper thin-film tensile properties: a reactive" + " molecular dynamics study. Journal of Applied Physics, 118:235306, " + "Dec 2015. URL: https://doi.org/10.1063/1.4938384, doi:10.1063/1.4938384. " + "This article has 8 citations and is from a peer-reviewed journal." + ), + }, + { + "title": "PaperQA: Retrieval-Augmented Generative Agent for Scientific Research", + "source": ["semantic_scholar"], + "key": "lala2023paperqaretrievalaugmentedgenerative", + "doi": "10.48550/arxiv.2312.07559", + "doc_id": "bb985e0e3265d678", + "journal": "ArXiv", + "authors": [ + "Jakub L'ala", + "Odhran O'Donoghue", + "Aleksandar Shtedritski", + "Sam Cox", + "Samuel G. Rodriques", + "Andrew D. White", + ], + "formatted_citation": ( + "Jakub L'ala, Odhran O'Donoghue, Aleksandar Shtedritski, Sam Cox, Samuel G. Rodriques," + " and Andrew D. White. Paperqa: retrieval-augmented generative agent for scientific " + "research. ArXiv, Dec 2023. URL: https://doi.org/10.48550/arxiv.2312.07559, " + "doi:10.48550/arxiv.2312.07559. This article has 21 citations." + ), + }, + { + "title": "Augmenting large language models with chemistry tools", + "source": ["semantic_scholar", "crossref"], + "key": "bran2024augmentinglargelanguage", + "doi": "10.1038/s42256-024-00832-8", + "doc_id": "0f650d59b0a2ba5a", + "journal": "Nature Machine Intelligence", + "authors": [ + "Andres M. Bran", + "Sam Cox", + "Oliver Schilter", + "Carlo Baldassari", + "Andrew D. White", + "Philippe Schwaller", + ], + "formatted_citation": ( + "Andres M. Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D. White, and " + "Philippe Schwaller. Augmenting large language models with chemistry tools. Nature " + "Machine Intelligence, 6:525-535, May 2024. URL: https://doi.org/10.1038/s42256-024-00832-8, " + "doi:10.1038/s42256-024-00832-8. This article has 187 citations and is from a " + "domain leading peer-reviewed journal." + ), + }, + ], +) +@pytest.mark.asyncio() +async def test_title_search(paper_attributes: dict[str, str]): + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query(title=paper_attributes["title"]) + assert set(details.other["client_source"]) == set( # type: ignore[union-attr] + paper_attributes["source"] + ), "Should have the correct source" + for key, value in paper_attributes.items(): + if key != "source": + assert getattr(details, key) == value, f"Should have the correct {key}" + + +@pytest.mark.vcr() +@pytest.mark.parametrize( + ("paper_attributes"), + [ + { + "title": "High-throughput screening of human genetic variants by pooled prime editing", + "source": ["semantic_scholar", "crossref"], + "key": "herger2024highthroughputscreeningof", + "doi": "10.1101/2024.04.01.587366", + "doc_id": "8e7669b50f31c52b", + "journal": "bioRxiv", + "authors": [ + "Michael Herger", + "Christina M. Kajba", + "Megan Buckley", + "Ana Cunha", + "Molly Strom", + "Gregory M. Findlay", + ], + "formatted_citation": ( + "Michael Herger, Christina M. Kajba, Megan Buckley, Ana Cunha, Molly Strom, " + "and Gregory M. Findlay. High-throughput screening of human genetic variants " + "by pooled prime editing. bioRxiv, Apr 2024. URL: https://doi.org/10.1101/2024.04.01.587366, " + "doi:10.1101/2024.04.01.587366. This article has 1 citations." + ), + }, + { + "title": ( + "An essential role of active site arginine residue in iodide binding and histidine residue " + "in electron transfer for iodide oxidation by horseradish peroxidase" + ), + "source": ["semantic_scholar", "crossref"], + "key": "adak2001anessentialrole", + "doi": "10.1023/a:1007154515475", + "doc_id": "3012c6676b658a27", + "journal": "Molecular and Cellular Biochemistry", + "authors": [ + "Subrata Adak", + "Debashis Bandyopadhyay", + "Uday Bandyopadhyay", + "Ranajit K. Banerjee", + ], + "formatted_citation": ( + "Subrata Adak, Debashis Bandyopadhyay, Uday Bandyopadhyay, and Ranajit K. Banerjee. " + "An essential role of active site arginine residue in iodide binding and histidine residue " + "in electron transfer for iodide oxidation by horseradish peroxidase. Molecular and Cellular " + "Biochemistry, 218:1-11, Feb 2001. URL: https://doi.org/10.1023/a:1007154515475, " + "doi:10.1023/a:1007154515475. This article has 7 citations and is from a peer-reviewed journal." + ), + }, + { + "title": "Convalescent-anti-sars-cov-2-plasma/immune-globulin", + "source": ["semantic_scholar", "crossref"], + "key": "unknownauthors2023convalescentantisarscov2plasmaimmuneglobulin", + "doi": "10.1007/s40278-023-41815-2", + "doc_id": "c2a60b772778732c", + "journal": "Reactions Weekly", + "authors": [], + "formatted_citation": ( + "Unknown author(s). Convalescent-anti-sars-cov-2-plasma/immune-globulin. Reactions Weekly, " + "1962:145-145, Jun 2023. URL: https://doi.org/10.1007/s40278-023-41815-2, " + "doi:10.1007/s40278-023-41815-2. This article has 0 citations and is from a peer-reviewed journal." + ), + }, + ], +) +@pytest.mark.asyncio() +async def test_doi_search(paper_attributes: dict[str, str]): + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query(doi=paper_attributes["doi"]) + assert set(details.other["client_source"]) == set( # type: ignore[union-attr] + paper_attributes["source"] + ), "Should have the correct source" + for key, value in paper_attributes.items(): + if key != "source": + assert getattr(details, key) == value, f"Should have the correct {key}" + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_bulk_doi_search(): + dois = [ + "10.1063/1.4938384", + "10.48550/arxiv.2312.07559", + "10.1038/s42256-024-00832-8", + "10.1101/2024.04.01.587366", + "10.1023/a:1007154515475", + "10.1007/s40278-023-41815-2", + ] + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.bulk_query([{"doi": doi} for doi in dois]) + assert len(details) == 6, "Should return 6 results" + assert all(d for d in details), "All results should be non-None" + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_bulk_title_search(): + titles = [ + "Effect of native oxide layers on copper thin-film tensile properties: A reactive molecular dynamics study", + "PaperQA: Retrieval-Augmented Generative Agent for Scientific Research", + "Augmenting large language models with chemistry tools", + "High-throughput screening of human genetic variants by pooled prime editing", + ( + "An essential role of active site arginine residue in iodide binding and histidine residue " + "in electron transfer for iodide oxidation by horseradish peroxidase" + ), + "Convalescent-anti-sars-cov-2-plasma/immune-globulin", + ] + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.bulk_query([{"title": title} for title in titles]) + assert len(details) == 6, "Should return 6 results" + assert all(d for d in details), "All results should be non-None" + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_bad_titles(): + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query(title="askldjrq3rjaw938h") + assert not details, "Should return None for bad title" + details = await client.query( + title="Effect of native oxide layers on copper thin-film tensile properties: A study" + ) + assert details, "Should find a similar title" + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_bad_dois(): + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query(title="abs12032jsdafn") + assert not details, "Should return None for bad doi" + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_minimal_fields_filtering(): + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query( + title="Augmenting large language models with chemistry tools", + fields=["title", "doi"], + ) + assert not details.journal, "Journal should not be populated" # type: ignore[union-attr] + assert not details.year, "Year should not be populated" # type: ignore[union-attr] + assert not details.authors, "Authors should not be populated" # type: ignore[union-attr] + assert details.citation == ( # type: ignore[union-attr] + "Unknown author(s). Augmenting large language models with chemistry tools." + " Unknown journal, Unknown year. URL: https://doi.org/10.1038/s42256-024-00832-8, " + "doi:10.1038/s42256-024-00832-8." + ), "Citation should be populated" + assert set(details.other["client_source"]) == { # type: ignore[union-attr] + "semantic_scholar", + "crossref", + }, "Should be from two sources" + assert not details.source_quality, "No source quality data should exist" # type: ignore[union-attr] + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_s2_only_fields_filtering(): + async with aiohttp.ClientSession() as session: + # now get with authors just from one source + s2_client = DocMetadataClient(session, clients=[SemanticScholarProvider]) + s2_details = await s2_client.query( + title="Augmenting large language models with chemistry tools", + fields=["title", "doi", "authors"], + ) + assert s2_details.authors, "Authors should be populated" # type: ignore[union-attr] + assert set(s2_details.other["client_source"]) == {"semantic_scholar"} # type: ignore[union-attr] + assert s2_details.citation == ( # type: ignore[union-attr] + "Andrés M Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D. White, " + "and P. Schwaller. Augmenting large language models with chemistry tools. " + "Unknown journal, Unknown year. URL: https://doi.org/10.1038/s42256-024-00832-8, " + "doi:10.1038/s42256-024-00832-8." + ), "Citation should be populated" + assert not s2_details.source_quality, "No source quality data should exist" # type: ignore[union-attr] + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_crossref_journalquality_fields_filtering(): + async with aiohttp.ClientSession() as session: + crossref_client = DocMetadataClient( + session, + clients=cast( + Collection[ + type[MetadataPostProcessor[Any]] | type[MetadataProvider[Any]] + ], + [CrossrefProvider, JournalQualityPostProcessor], + ), + ) + crossref_details = await crossref_client.query( + title="Augmenting large language models with chemistry tools", + fields=["title", "doi", "authors", "journal"], + ) + assert set(crossref_details.other["client_source"]) == { # type: ignore[union-attr] + "crossref" + }, "Should be from only crossref" + assert crossref_details.source_quality == 2, "Should have source quality data" # type: ignore[union-attr] + assert crossref_details.citation == ( # type: ignore[union-attr] + "Andres M. Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D. White, " + "and Philippe Schwaller. Augmenting large language models with chemistry tools. " + "Nature Machine Intelligence, Unknown year. URL: https://doi.org/10.1038/s42256-024-00832-8, " + "doi:10.1038/s42256-024-00832-8." + ), "Citation should be populated" + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_author_matching(): + async with aiohttp.ClientSession() as session: + crossref_client = DocMetadataClient(session, clients=[CrossrefProvider]) + s2_client = DocMetadataClient(session, clients=[SemanticScholarProvider]) + crossref_details_bad_author = await crossref_client.query( + title="Augmenting large language models with chemistry tools", + authors=["Jack NoScience"], + fields=["title", "doi", "authors"], + ) + + s2_details_bad_author = await s2_client.query( + title="Augmenting large language models with chemistry tools", + authors=["Jack NoScience"], + fields=["title", "doi", "authors"], + ) + + s2_details_w_author = await s2_client.query( + title="Augmenting large language models with chemistry tools", + authors=["Andres M. Bran", "Sam Cox"], + fields=["title", "doi", "authors"], + ) + + assert not crossref_details_bad_author, "Should return None for bad author" + assert not s2_details_bad_author, "Should return None for bad author" + assert s2_details_w_author, "Should return results for good author" + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_odd_client_requests(): + # try querying using an authors match, but not requesting authors back + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query( + title="Augmenting large language models with chemistry tools", + authors=["Andres M. Bran", "Sam Cox"], + fields=["title", "doi"], + ) + assert ( + details.authors # type: ignore[union-attr] + ), "Should return correct author results" + + # try querying using a title, asking for no DOI back + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query( + title="Augmenting large language models with chemistry tools", + fields=["title"], + ) + assert ( + details.doi # type: ignore[union-attr] + ), "Should return a doi even though we don't ask for it" + + # try querying using a title, asking for no title back + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query( + title="Augmenting large language models with chemistry tools", + fields=["doi"], + ) + assert ( + details.title # type: ignore[union-attr] + ), "Should return a title even though we don't ask for it" + + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query( + doi="10.1007/s40278-023-41815-2", + fields=["doi", "title", "gibberish-field", "no-field"], + ) + assert ( + details.title # type: ignore[union-attr] + ), "Should return title even though we asked for some bad fields" + + +@pytest.mark.asyncio() +async def test_ensure_robust_to_timeouts(monkeypatch): + # 0.15 should be short enough to not get a response in time. + monkeypatch.setattr(paperqa.clients.crossref, "CROSSREF_API_REQUEST_TIMEOUT", 0.05) + monkeypatch.setattr( + paperqa.clients.semantic_scholar, "SEMANTIC_SCHOLAR_API_REQUEST_TIMEOUT", 0.05 + ) + + async with aiohttp.ClientSession() as session: + client = DocMetadataClient(session) + details = await client.query( + doi="10.1007/s40278-023-41815-2", + fields=["doi", "title"], + ) + assert details is None, "Should return None for timeout" + + +@pytest.mark.asyncio() +async def test_bad_init(): + with pytest.raises( + ValueError, match="At least one MetadataProvider must be provided." + ): + client = DocMetadataClient(clients=[]) # noqa: F841 + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_ensure_sequential_run(caplog): + caplog.set_level(logging.DEBUG) + # were using a DOI that is NOT in crossref, but running the crossref client first + # we will ensure that both are run sequentially + + async with aiohttp.ClientSession() as session: + client = DocMetadataClient( + session=session, + clients=cast( + Sequence[ + Collection[ + type[MetadataPostProcessor[Any]] | type[MetadataProvider[Any]] + ] + ], + [[CrossrefProvider], [SemanticScholarProvider]], + ), + ) + details = await client.query( + doi="10.48550/arxiv.2312.07559", + fields=["doi", "title"], + ) + assert details, "Should find the right DOI in the second client" + record_indices = {"crossref": -1, "semantic_scholar": -1} + for n, record in enumerate(caplog.records): + if "CrossrefProvider" in record.msg: + record_indices["crossref"] = n + if "SemanticScholarProvider" in record.msg: + record_indices["semantic_scholar"] = n + assert ( + record_indices["crossref"] < record_indices["semantic_scholar"] + ), "Crossref should run first" + + +@pytest.mark.vcr() +@pytest.mark.asyncio() +async def test_ensure_sequential_run_early_stop(caplog): + caplog.set_level(logging.DEBUG) + # now we should stop after hitting s2 + async with aiohttp.ClientSession() as session: + client = DocMetadataClient( + session=session, + clients=cast( + Sequence[ + Collection[ + type[MetadataPostProcessor[Any]] | type[MetadataProvider[Any]] + ] + ], + [[SemanticScholarProvider], [CrossrefProvider]], + ), + ) + details = await client.query( + doi="10.48550/arxiv.2312.07559", + fields=["doi", "title"], + ) + assert details, "Should find the right DOI in the second client" + record_indices = {"crossref": -1, "semantic_scholar": -1, "early_stop": -1} + for n, record in enumerate(caplog.records): + if "CrossrefProvider" in record.msg: + record_indices["crossref"] = n + if "SemanticScholarProvider" in record.msg: + record_indices["semantic_scholar"] = n + if "stopping early." in record.msg: + record_indices["early_stop"] = n + assert ( + record_indices["crossref"] == -1 + ), "Crossref should be index -1 i.e. not found" + assert ( + record_indices["semantic_scholar"] != -1 + ), "Semantic Scholar should be found" + assert record_indices["early_stop"] != -1, "We should stop early." diff --git a/tests/test_paperqa.py b/tests/test_paperqa.py index 97fbb49f..3bc8efb7 100644 --- a/tests/test_paperqa.py +++ b/tests/test_paperqa.py @@ -23,6 +23,7 @@ Text, print_callback, ) +from paperqa.clients import CrossrefProvider from paperqa.llms import ( AnthropicLLMModel, EmbeddingModel, @@ -1324,6 +1325,48 @@ def test_pdf_reader(): assert "yes" in answer.answer or "Yes" in answer.answer +def test_pdf_reader_w_no_match_doc_details(): + tests_dir = os.path.dirname(os.path.abspath(__file__)) + doc_path = os.path.join(tests_dir, "paper.pdf") + docs = Docs(llm_model=OpenAILLMModel(config={"temperature": 0.0, "model": "gpt-4"})) + docs.add(doc_path, "Wellawatte et al, XAI Review, 2023", use_doc_details=True) # type: ignore[arg-type] + # doc will be a DocDetails object, but nothing can be found + # thus, we retain the prior citation data + assert ( + next(iter(docs.docs.values())).citation == "Wellawatte et al, XAI Review, 2023" + ) + answer = docs.query("Are counterfactuals actionable? [yes/no]") + assert "yes" in answer.answer or "Yes" in answer.answer + + +def test_pdf_reader_match_doc_details(): + tests_dir = os.path.dirname(os.path.abspath(__file__)) + doc_path = os.path.join(tests_dir, "paper.pdf") + docs = Docs(llm_model=OpenAILLMModel(config={"temperature": 0.0, "model": "gpt-4"})) + # we limit to only crossref since s2 is too flaky + docs.add( + doc_path, # type: ignore[arg-type] + "Wellawatte et al, A Perspective on Explanations of Molecular Prediction Models, XAI Review, 2023", + use_doc_details=True, + clients={CrossrefProvider}, + fields=["author", "journal"], + ) + doc_details = next(iter(docs.docs.values())) + assert doc_details.dockey == "5300ef1d5fb960d7" + # note year is unknown because citation string is only parsed for authors/title/doi + # AND we do not request it back from the metadata sources + assert doc_details.docname == "wellawatteUnknownyearaperspectiveon" + assert set(doc_details.authors) == { # type: ignore[attr-defined] + "Geemi P. Wellawatte", + "Heta A. Gandhi", + "Aditi Seshadri", + "Andrew D. White", + } + assert doc_details.doi == "10.26434/chemrxiv-2022-qfv02" # type: ignore[attr-defined] + answer = docs.query("Are counterfactuals actionable? [yes/no]") + assert "yes" in answer.answer or "Yes" in answer.answer + + def test_fileio_reader_pdf(): tests_dir = os.path.dirname(os.path.abspath(__file__)) doc_path = os.path.join(tests_dir, "paper.pdf")