diff --git a/src/institution/migrations/0005_alter_institution_associated_institutions_and_more.py b/src/institution/migrations/0005_alter_institution_associated_institutions_and_more.py new file mode 100644 index 000000000..93c2288eb --- /dev/null +++ b/src/institution/migrations/0005_alter_institution_associated_institutions_and_more.py @@ -0,0 +1,42 @@ +# Generated by Django 4.1 on 2024-05-20 19:24 + +import django.contrib.postgres.fields +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("institution", "0004_institution_openalex_created_date_and_more"), + ] + + operations = [ + migrations.AlterField( + model_name="institution", + name="associated_institutions", + field=django.contrib.postgres.fields.ArrayField( + base_field=models.CharField(blank=True, max_length=500, null=True), + size=None, + ), + ), + migrations.AlterField( + model_name="institution", + name="h_index", + field=models.IntegerField(blank=True, default=0, null=True), + ), + migrations.AlterField( + model_name="institution", + name="i10_index", + field=models.IntegerField(blank=True, default=0, null=True), + ), + migrations.AlterField( + model_name="institution", + name="two_year_mean_citedness", + field=models.FloatField(blank=True, default=0, null=True), + ), + migrations.AlterField( + model_name="institution", + name="works_count", + field=models.IntegerField(blank=True, default=0, null=True), + ), + ] diff --git a/src/institution/models.py b/src/institution/models.py index 841c5d4b7..a0fc55d1b 100644 --- a/src/institution/models.py +++ b/src/institution/models.py @@ -89,20 +89,20 @@ class Institution(DefaultModel): ) # https://docs.openalex.org/api-entities/institutions/institution-object#2yr_mean_citedness - two_year_mean_citedness = models.FloatField(blank=False, null=False, default=0) + two_year_mean_citedness = models.FloatField(blank=True, null=True, default=0) # https://docs.openalex.org/api-entities/institutions/institution-object#summary_stats - h_index = models.IntegerField(blank=False, null=False, default=0) + h_index = models.IntegerField(blank=True, null=True, default=0) # https://docs.openalex.org/api-entities/institutions/institution-object#summary_stats - i10_index = models.IntegerField(blank=False, null=False, default=0) + i10_index = models.IntegerField(blank=True, null=True, default=0) # https://docs.openalex.org/api-entities/institutions/institution-object#works_count - works_count = models.IntegerField(blank=False, null=False, default=0) + works_count = models.IntegerField(blank=True, null=True, default=0) # https://docs.openalex.org/api-entities/institutions/institution-object#associated_institutions associated_institutions = ArrayField( - models.CharField(blank=False, null=False, max_length=500) + models.CharField(blank=True, null=True, max_length=500) ) # https://docs.openalex.org/api-entities/institutions/institution-object#display_name_alternatives @@ -164,11 +164,12 @@ def upsert_from_openalex(oa_institution): "works_count": oa_institution.get("works_count"), "associated_institutions": list( map( - lambda obj: obj["id"], oa_institution.get("associated_institutions") + lambda obj: obj["id"], + oa_institution.get("associated_institutions", []), ) ), "display_name_alternatives": oa_institution.get( - "display_name_alternatives" + "display_name_alternatives", [] ), } @@ -176,6 +177,6 @@ def upsert_from_openalex(oa_institution): for key, value in mapped.items(): setattr(institution, key, value) institution.save() - else: + elif not institution: institution = Institution.objects.create(**mapped) return institution diff --git a/src/institution/serializers.py b/src/institution/serializers.py new file mode 100644 index 000000000..940352575 --- /dev/null +++ b/src/institution/serializers.py @@ -0,0 +1,12 @@ +from rest_framework.serializers import SerializerMethodField + +from institution.models import Institution +from researchhub.serializers import DynamicModelFieldSerializer + + +class DynamicInstitutionSerializer(DynamicModelFieldSerializer): + institutions = SerializerMethodField() + + class Meta: + model = Institution + fields = "__all__" diff --git a/src/paper/openalex_util.py b/src/paper/openalex_util.py index 2ecae9fe7..4af4efbc5 100644 --- a/src/paper/openalex_util.py +++ b/src/paper/openalex_util.py @@ -1,16 +1,16 @@ +import copy import logging -from django.apps import apps -from django.core.cache import cache from django.core.exceptions import ValidationError from django.db import IntegrityError, transaction from django.db.models import Q import utils.sentry as sentry -from paper.utils import get_cache_key -from purchase.models import Wallet -from tag.models import Concept -from utils.http import check_url_contains_pdf +from user.related_models.author_contribution_summary_model import ( + AuthorContributionSummary, +) +from user.related_models.author_institution import AuthorInstitution +from user.related_models.coauthor_model import CoAuthor from utils.openalex import OpenAlex # Only these particular fields will be updated when an OpenAlex @@ -66,7 +66,15 @@ def process_openalex_works(works): # Split works into two buckets: create and update create_papers = [] update_papers = [] + for work in works: + # When fetched in batch, OpneAlex will truncate authors beyond 100. + # If this is the case, we need to fetch the full work + # https://docs.openalex.org/api-entities/authors/limitations + if work.get("is_authors_truncated", False): + just_id = work.get("id").split("/")[-1] + work = open_alex.get_work(just_id) + doi = work.get("doi") if doi is None: print(f"No Doi for result: {work.get('id')}") @@ -82,53 +90,58 @@ def process_openalex_works(works): else: create_papers.append(work) - paper_to_topics_and_concepts = {} + paper_to_openalex_data = {} # Create new papers - with transaction.atomic(): - for work in create_papers: - ( - data, - openalex_concepts, - openalex_topics, - ) = open_alex.build_paper_from_openalex_work(work) + for work in create_papers: + _work = copy.deepcopy(work) + ( + data, + openalex_concepts, + openalex_topics, + ) = open_alex.build_paper_from_openalex_work(_work) - paper = Paper(**data) + paper = Paper(**data) - # Validate paper - try: - paper.clean_fields() - paper.clean() - except ValidationError as e: - sentry.log_error( - e, - message=f"Failed to validate paper: {paper.doi}, {work.get('id')}", - ) - continue + # Validate paper + try: + paper.clean_fields() + paper.clean() + except ValidationError as e: + sentry.log_error( + e, + message=f"Failed to validate paper: {paper.doi}, {work.get('id')}", + ) + continue - try: - paper.save() - except IntegrityError as e: - sentry.log_error( - e, message=f"Failed to save paper, DOI already exists: {paper.doi}" - ) - except Exception as e: - sentry.log_error( - e, message=f"Failed to save paper, unexpected error: {paper.doi}" - ) + try: + paper.save() - paper_to_topics_and_concepts[paper.id] = ( - openalex_concepts, - openalex_topics, + # Succeessfully saved paper, add to map + paper_to_openalex_data[paper.id] = { + "openalex_concepts": openalex_concepts, + "openalex_topics": openalex_topics, + "openalex_work": work, + } + except IntegrityError as e: + sentry.log_error( + e, message=f"Failed to save paper, DOI already exists: {paper.doi}" ) + continue + except Exception as e: + sentry.log_error( + e, message=f"Failed to save paper, unexpected error: {paper.doi}" + ) + continue # Prepare papers for batch update for existing_paper, work in update_papers: + _work = copy.deepcopy(work) ( data, openalex_concepts, openalex_topics, - ) = open_alex.build_paper_from_openalex_work(work) + ) = open_alex.build_paper_from_openalex_work(_work) # we didn't fetch all fields in the initial paper query (we used .only()), # so we need to explicitly fetch them if we want to update them. @@ -138,10 +151,11 @@ def process_openalex_works(works): for field in PAPER_FIELDS_ALLOWED_TO_UPDATE: setattr(existing_paper, field, data.get(field)) - paper_to_topics_and_concepts[existing_paper.id] = ( - openalex_concepts, - openalex_topics, - ) + paper_to_openalex_data[existing_paper.id] = { + "openalex_concepts": openalex_concepts, + "openalex_topics": openalex_topics, + "openalex_work": work, + } # perform batch update if update_papers and len(update_papers) > 0: @@ -153,6 +167,161 @@ def process_openalex_works(works): sentry.log_error(e, message="Failed to bulk update papers") # Upsert concepts and associate to papers - for paper_id, topics_and_concepts in paper_to_topics_and_concepts.items(): - openalex_concepts, openalex_topics = topics_and_concepts - create_paper_related_tags(paper_id, openalex_concepts, openalex_topics) + for paper_id, paper_data in paper_to_openalex_data.items(): + print("processing work: " + paper_data["openalex_work"]["id"]) + work = paper_data["openalex_work"] + + create_paper_related_tags( + paper_id, paper_data["openalex_concepts"], paper_data["openalex_topics"] + ) + + openalex_authorships = work.get("authorships") + if openalex_authorships and paper_id: + try: + process_openalex_authorships(openalex_authorships, paper_id) + except Exception as e: + sentry.log_error( + e, message=f"Failed to process authorships for paper_id: {paper_id}" + ) + else: + sentry.log_error( + None, + message=f"Authorships data is missing or paper_id is None for work: {work.get('id')}", + ) + + +def process_openalex_authorships(openalex_authorships, related_paper_id): + """ + Iterates through authorships associated with an OpenAlex work and create related objects such as + AuthorInstitution, Authorship, and Author objects. Related models will be updated if they already exist. + https://docs.openalex.org/api-entities/works/work-object/authorship-object + """ + from institution.models import Institution + from paper.models import Paper + from paper.related_models.authorship_model import Authorship + from purchase.models import Wallet + from user.related_models.author_model import Author + + open_alex = OpenAlex() + related_paper = Paper.objects.get(id=related_paper_id) + + authors_need_additional_data_fetch = [] + authors_in_this_work = [] + for oa_authorship in openalex_authorships: + author_position = oa_authorship.get("author_position") + author_openalex_id = oa_authorship.get("author", {}).get("id") + + just_id = author_openalex_id.split("/")[-1] + authors_need_additional_data_fetch.append(just_id) + + author = None + try: + author = Author.objects.get(openalex_ids__contains=[author_openalex_id]) + except Author.DoesNotExist: + author_name_parts = ( + oa_authorship.get("author", {}).get("display_name").split(" ") + ) + author = Author.objects.create( + first_name=author_name_parts[0], + last_name=author_name_parts[-1], + openalex_ids=[author_openalex_id], + created_source=Author.SOURCE_OPENALEX, + ) + Wallet.objects.create(author=author) + except Exception as e: + continue + + # Associate paper with author + related_paper.authors.add(author) + + # Find or create authorship + authorship, created = Authorship.objects.get_or_create( + author=author, + author_position=author_position, + paper=related_paper, + is_corresponding=oa_authorship.get("is_corresponding"), + raw_author_name=oa_authorship.get("author", {}).get("display_name"), + ) + + authors_in_this_work.append(author) + + # Set institutions associated with authorships if they do not already exist + for oa_inst in oa_authorship.get("institutions", []): + institution = Institution.upsert_from_openalex(oa_inst) + if institution: + authorship.institutions.add(institution) + + # Update authors with additional metadata from OpenAlex + oa_authors = [] + if len(authors_need_additional_data_fetch) > 0: + oa_authors, _ = open_alex.get_authors( + openalex_ids=authors_need_additional_data_fetch + ) + + for oa_author in oa_authors: + try: + author = Author.objects.get(openalex_ids__contains=[oa_author.get("id")]) + except Author.DoesNotExist as e: + # This should not happen but hey, anything can happen! + logging.warning( + f"Author with OpenAlex ID not found: {oa_author.get('id')}", + ) + sentry.log_error( + e, + message=f"Author with OpenAlex ID {oa_author.get('id')} not found", + ) + continue + + # Set misc author metadata + author.i10_index = oa_author.get("summary_stats", {}).get("i10_index") + author.h_index = oa_author.get("summary_stats", {}).get("h_index") + author.two_year_mean_citedness = oa_author.get("summary_stats", {}).get( + "2yr_mean_citedness" + ) + author.orcid_id = oa_author.get("orcid") + author.save() + + # Set author contribution/citation activity + activity_by_year = oa_author.get("counts_by_year", []) + for activity in activity_by_year: + try: + AuthorContributionSummary.objects.update_or_create( + source=AuthorContributionSummary.SOURCE_OPENALEX, + author=author, + year=activity.get("year"), + defaults={ + "works_count": activity.get("works_count", None), + "citation_count": activity.get("cited_by_count", None), + }, + ) + except Exception as e: + sentry.log_error( + e, + message=f"Failed to upsert author contribution summary for author: {str(author.id)}", + ) + + # Load all the institutions author is associated with + affiliations = oa_author.get("affiliations", []) + for affiliation in affiliations: + oa_institution = affiliation.get("institution") + years = affiliation.get("years", []) + + institution = None + try: + institution = Institution.objects.get(openalex_id=oa_institution["id"]) + except Institution.DoesNotExist as e: + continue + + author_inst = AuthorInstitution.objects.get_or_create( + author=author, + institution=institution, + years=years, + ) + + # Create co-author relationships + for i, author in enumerate(authors_in_this_work): + for coauthor in authors_in_this_work: + if author != coauthor: + CoAuthor.objects.get_or_create( + author=author, coauthor=coauthor, paper_id=related_paper_id + ) diff --git a/src/paper/paper_upload_tasks.py b/src/paper/paper_upload_tasks.py index 6e4450a8b..5f97d3b78 100644 --- a/src/paper/paper_upload_tasks.py +++ b/src/paper/paper_upload_tasks.py @@ -707,13 +707,17 @@ def create_paper_related_tags(paper_id, openalex_concepts=[], openalex_topics=[] with transaction.atomic(): biorxiv_hub_id = 436 - try: - paper.hubs.add(biorxiv_hub_id) - paper.unified_document.hubs.add(biorxiv_hub_id) - except Exception as e: - sentry.log_error( - e, message=f"Failed to add paper to biorXiv hub: {paper.id}" - ) + if Hub.objects.filter(id=biorxiv_hub_id).exists(): + try: + paper.hubs.add(biorxiv_hub_id) + paper.unified_document.hubs.add(biorxiv_hub_id) + except Exception as e: + sentry.log_error( + e, message=f"Failed to add paper to biorXiv hub: {paper.id}" + ) + else: + # bioRxiv hub does not exist. This must be a staging / dev environment + pass @app.task(queue=QUEUE_PAPER_METADATA) diff --git a/src/paper/tests/openalex_authors.json b/src/paper/tests/openalex_authors.json new file mode 100644 index 000000000..a0683c762 --- /dev/null +++ b/src/paper/tests/openalex_authors.json @@ -0,0 +1,1309 @@ +{ + "meta": { + "count": 1, + "db_response_time_ms": 15, + "page": 1, + "per_page": 25, + "groups_count": null + }, + "results": [ + { + "id": "https://openalex.org/A5053648717", + "orcid": "https://orcid.org/0000-0001-5679-8902", + "display_name": "Matthias Ernzerhof", + "display_name_alternatives": [ + "M. Ernzerhof", + "Matthias Ernzerhof" + ], + "works_count": 119, + "cited_by_count": 205672, + "summary_stats": { + "2yr_mean_citedness": 2.0, + "h_index": 35, + "i10_index": 72 + }, + "ids": { + "openalex": "https://openalex.org/A5053648717", + "orcid": "https://orcid.org/0000-0001-5679-8902" + }, + "affiliations": [ + { + "institution": { + "id": "https://openalex.org/I70931966", + "ror": "https://ror.org/0161xgx34", + "display_name": "Universit\u00e9 de Montr\u00e9al", + "country_code": "CA", + "type": "education", + "lineage": [ + "https://openalex.org/I70931966" + ] + }, + "years": [ + 2023, + 2022, + 2021, + 2020, + 2019, + 2018, + 2017, + 2016, + 2015, + 2014 + ] + }, + { + "institution": { + "id": "https://openalex.org/I4210115901", + "ror": "https://ror.org/029dwxd81", + "display_name": "Centre in Green Chemistry and Catalysis", + "country_code": "CA", + "type": "facility", + "lineage": [ + "https://openalex.org/I4210115901" + ] + }, + "years": [ + 2021, + 2019 + ] + }, + { + "institution": { + "id": "https://openalex.org/I159129438", + "ror": "https://ror.org/002rjbv21", + "display_name": "Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al", + "country_code": "CA", + "type": "education", + "lineage": [ + "https://openalex.org/I159129438", + "https://openalex.org/I49663120" + ] + }, + "years": [ + 2020 + ] + }, + { + "institution": { + "id": "https://openalex.org/I4210099103", + "ror": "https://ror.org/010rs2a38", + "display_name": "D\u00e9partement de Chimie Mol\u00e9culaire", + "country_code": "FR", + "type": "facility", + "lineage": [ + "https://openalex.org/I1294671590", + "https://openalex.org/I4210099103", + "https://openalex.org/I4210128300" + ] + }, + "years": [ + 2019 + ] + }, + { + "institution": { + "id": "https://openalex.org/I4210144791", + "ror": "https://ror.org/04dbzz632", + "display_name": "Institut N\u00e9el", + "country_code": "FR", + "type": "facility", + "lineage": [ + "https://openalex.org/I1294671590", + "https://openalex.org/I4210098836", + "https://openalex.org/I4210144791", + "https://openalex.org/I899635006" + ] + }, + "years": [ + 2013 + ] + }, + { + "institution": { + "id": "https://openalex.org/I114832834", + "ror": "https://ror.org/04vmvtb21", + "display_name": "Tulane University", + "country_code": "US", + "type": "education", + "lineage": [ + "https://openalex.org/I114832834" + ] + }, + "years": [ + 2008, + 1998, + 1997, + 1996 + ] + }, + { + "institution": { + "id": "https://openalex.org/I74775410", + "ror": "https://ror.org/008zs3103", + "display_name": "Rice University", + "country_code": "US", + "type": "education", + "lineage": [ + "https://openalex.org/I74775410" + ] + }, + "years": [ + 2001, + 2000, + 1999 + ] + }, + { + "institution": { + "id": "https://openalex.org/I4210094722", + "ror": "https://ror.org/00tbs6p91", + "display_name": "Center for Nanoscale Science and Technology", + "country_code": "US", + "type": "government", + "lineage": [ + "https://openalex.org/I1321296531", + "https://openalex.org/I1343035065", + "https://openalex.org/I4210094722" + ] + }, + "years": [ + 2001 + ] + }, + { + "institution": { + "id": "https://openalex.org/I135140700", + "ror": "https://ror.org/041nas322", + "display_name": "University of Bonn", + "country_code": "DE", + "type": "education", + "lineage": [ + "https://openalex.org/I135140700" + ] + }, + "years": [ + 1996, + 1994, + 1992 + ] + }, + { + "institution": { + "id": "https://openalex.org/I62916508", + "ror": "https://ror.org/02kkvpp62", + "display_name": "Technical University of Munich", + "country_code": "DE", + "type": "education", + "lineage": [ + "https://openalex.org/I62916508" + ] + }, + "years": [ + 1996, + 1995 + ] + } + ], + "last_known_institutions": [ + { + "id": "https://openalex.org/I70931966", + "ror": "https://ror.org/0161xgx34", + "display_name": "Universit\u00e9 de Montr\u00e9al", + "country_code": "CA", + "type": "education", + "lineage": [ + "https://openalex.org/I70931966" + ] + } + ], + "topics": [ + { + "id": "https://openalex.org/T10002", + "display_name": "Advancements in Density Functional Theory", + "count": 63, + "subfield": { + "id": "https://openalex.org/subfields/3107", + "display_name": "Atomic and Molecular Physics, and Optics" + }, + "field": { + "id": "https://openalex.org/fields/31", + "display_name": "Physics and Astronomy" + }, + "domain": { + "id": "https://openalex.org/domains/3", + "display_name": "Physical Sciences" + } + }, + { + "id": "https://openalex.org/T10913", + "display_name": "Molecular Electronic Devices and Systems", + "count": 54, + "subfield": { + "id": "https://openalex.org/subfields/2208", + "display_name": "Electrical and Electronic Engineering" + }, + "field": { + "id": "https://openalex.org/fields/22", + "display_name": "Engineering" + }, + "domain": { + "id": "https://openalex.org/domains/3", + "display_name": "Physical Sciences" + } + }, + { + "id": "https://openalex.org/T11177", + "display_name": "Quantum Coherence in Photosynthesis and Aqueous Systems", + "count": 38, + "subfield": { + "id": "https://openalex.org/subfields/3107", + "display_name": "Atomic and Molecular Physics, and Optics" + }, + "field": { + "id": "https://openalex.org/fields/31", + "display_name": "Physics and Astronomy" + }, + "domain": { + "id": "https://openalex.org/domains/3", + "display_name": "Physical Sciences" + } + }, + { + "id": "https://openalex.org/T10382", + "display_name": "Semiconductor Spintronics and Quantum Computing", + "count": 24, + "subfield": { + "id": "https://openalex.org/subfields/3107", + "display_name": "Atomic and Molecular Physics, and Optics" + }, + "field": { + "id": "https://openalex.org/fields/31", + "display_name": "Physics and Astronomy" + }, + "domain": { + "id": "https://openalex.org/domains/3", + "display_name": "Physical Sciences" + } + }, + { + "id": "https://openalex.org/T10045", + "display_name": "Organic Solar Cell Technology", + "count": 10, + "subfield": { + "id": "https://openalex.org/subfields/2208", + "display_name": "Electrical and Electronic Engineering" + }, + "field": { + "id": "https://openalex.org/fields/22", + "display_name": "Engineering" + }, + "domain": { + "id": "https://openalex.org/domains/3", + "display_name": "Physical Sciences" + } + }, + { + "id": "https://openalex.org/T10083", + "display_name": "Graphene: Properties, Synthesis, and Applications", + "count": 9, + "subfield": { + "id": "https://openalex.org/subfields/2505", + "display_name": "Materials Chemistry" + }, + "field": { + "id": "https://openalex.org/fields/25", + "display_name": "Materials Science" + }, + "domain": { + "id": "https://openalex.org/domains/3", + "display_name": "Physical Sciences" + } + }, + { + "id": "https://openalex.org/T11809", + "display_name": "NMR Spectroscopy Techniques", + "count": 8, + "subfield": { + "id": "https://openalex.org/subfields/1607", + "display_name": "Spectroscopy" + }, + "field": { + "id": 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"cited_by_count": 13942 }, { "year": 2020, - "cited_by_count": 2560 + "cited_by_count": 13022 }, { "year": 2019, - "cited_by_count": 2469 + "cited_by_count": 12263 }, { "year": 2018, - "cited_by_count": 2690 + "cited_by_count": 11221 }, { "year": 2017, - "cited_by_count": 2767 + "cited_by_count": 9988 }, { "year": 2016, - "cited_by_count": 3085 + "cited_by_count": 8488 }, { "year": 2015, - "cited_by_count": 3545 + "cited_by_count": 7654 }, { "year": 2014, - "cited_by_count": 3906 + "cited_by_count": 6898 }, { "year": 2013, - "cited_by_count": 4387 + "cited_by_count": 6254 }, { "year": 2012, - "cited_by_count": 4254 + "cited_by_count": 5452 } ], - "updated_date": "2024-05-08T22:51:42.412644", + "updated_date": "2024-05-15T22:29:26.487685", "created_date": "2016-06-24" } ], diff --git a/src/paper/tests/test_process_openalex_works.py b/src/paper/tests/test_process_openalex_works.py index 4806731e2..baaf943a8 100644 --- a/src/paper/tests/test_process_openalex_works.py +++ b/src/paper/tests/test_process_openalex_works.py @@ -1,9 +1,15 @@ import json +from unittest.mock import patch from rest_framework.test import APITestCase from paper.models import Paper from paper.openalex_util import process_openalex_works +from user.related_models.author_contribution_summary_model import ( + AuthorContributionSummary, +) +from user.related_models.author_model import Author +from utils.openalex import OpenAlex class ProcessOpenAlexWorksTests(APITestCase): @@ -12,61 +18,196 @@ def setUp(self): response = json.load(file) self.works = response.get("results") - def test_create_papers_from_openalex_works(self): - process_openalex_works(self.works) + @patch.object(OpenAlex, "get_authors") + def test_create_papers_from_openalex_works(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) - dois = [work.get("doi") for work in self.works] - dois = [doi.replace("https://doi.org/", "") for doi in dois] + process_openalex_works(self.works) - created_papers = Paper.objects.filter(doi__in=dois) - self.assertEqual(len(created_papers), 2) + dois = [work.get("doi") for work in self.works] + dois = [doi.replace("https://doi.org/", "") for doi in dois] - def test_creating_papers_should_create_related_topics(self): - process_openalex_works(self.works) + created_papers = Paper.objects.filter(doi__in=dois) + self.assertEqual(len(created_papers), 2) - dois = [work.get("doi") for work in self.works] - dois = [doi.replace("https://doi.org/", "") for doi in dois] - created_papers = Paper.objects.filter(doi__in=dois) + @patch.object(OpenAlex, "get_authors") + def test_creating_papers_should_create_related_topics(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) - # Sample the first paper to ensure it has concepts - paper_concepts = created_papers.first().unified_document.concepts.all() - self.assertGreater(len(paper_concepts), 0) + process_openalex_works(self.works) - def test_creating_papers_should_create_related_concepts(self): - process_openalex_works(self.works) + dois = [work.get("doi") for work in self.works] + dois = [doi.replace("https://doi.org/", "") for doi in dois] + created_papers = Paper.objects.filter(doi__in=dois) - dois = [work.get("doi") for work in self.works] - dois = [doi.replace("https://doi.org/", "") for doi in dois] - created_papers = Paper.objects.filter(doi__in=dois) + # Sample the first paper to ensure it has concepts + paper_concepts = created_papers.first().unified_document.concepts.all() + self.assertGreater(len(paper_concepts), 0) - # Sample the first paper to ensure it has topics - paper_topics = created_papers.first().unified_document.topics.all() - self.assertGreater(len(paper_topics), 0) + @patch.object(OpenAlex, "get_authors") + def test_creating_papers_should_create_related_concepts(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) - def test_creating_papers_should_create_related_hubs(self): - process_openalex_works(self.works) + process_openalex_works(self.works) - dois = [work.get("doi") for work in self.works] - dois = [doi.replace("https://doi.org/", "") for doi in dois] - created_papers = Paper.objects.filter(doi__in=dois) + dois = [work.get("doi") for work in self.works] + dois = [doi.replace("https://doi.org/", "") for doi in dois] + created_papers = Paper.objects.filter(doi__in=dois) - # Sample the first paper to ensure it has topics - paper_hubs = created_papers.first().unified_document.hubs.all() - self.assertGreater(len(paper_hubs), 0) + # Sample the first paper to ensure it has topics + paper_topics = created_papers.first().unified_document.topics.all() + self.assertGreater(len(paper_topics), 0) - def test_updating_existing_papers_from_openalex_works(self): - # First create paper - work = self.works[0] - work["title"] = "Old title" - process_openalex_works([work]) + @patch.object(OpenAlex, "get_authors") + def test_creating_papers_should_create_related_hubs(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) - # Update paper - work["title"] = "New title" - process_openalex_works([work]) + process_openalex_works(self.works) - dois = [work.get("doi") for work in self.works] - dois = [doi.replace("https://doi.org/", "") for doi in dois] - updated_paper = Paper.objects.filter(doi__in=dois).first() + dois = [work.get("doi") for work in self.works] + dois = [doi.replace("https://doi.org/", "") for doi in dois] + created_papers = Paper.objects.filter(doi__in=dois) - self.assertEqual(updated_paper.title, "New title") - self.assertEqual(updated_paper.paper_title, "New title") + # Sample the first paper to ensure it has topics + paper_hubs = created_papers.first().unified_document.hubs.all() + self.assertGreater(len(paper_hubs), 0) + + @patch.object(OpenAlex, "get_authors") + def test_updating_existing_papers_from_openalex_works(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) + + # First create paper + work = self.works[0] + work["title"] = "Old title" + process_openalex_works([work]) + + # Update paper + work["title"] = "New title" + process_openalex_works([work]) + + dois = [work.get("doi") for work in self.works] + dois = [doi.replace("https://doi.org/", "") for doi in dois] + updated_paper = Paper.objects.filter(doi__in=dois).first() + + self.assertEqual(updated_paper.title, "New title") + self.assertEqual(updated_paper.paper_title, "New title") + + @patch.object(OpenAlex, "get_authors") + def test_create_authors_when_processing_work(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) + + process_openalex_works(self.works) + + dois = [work.get("doi") for work in self.works] + dois = [doi.replace("https://doi.org/", "") for doi in dois] + created_papers = Paper.objects.filter(doi__in=dois) + + # Sample the first paper to ensure it has authors + paper_authors = created_papers.first().authors.all() + self.assertGreater(len(paper_authors), 0) + + @patch.object(OpenAlex, "get_authors") + def test_create_authorships_when_processing_work(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) + + process_openalex_works(self.works) + + dois = [work.get("doi") for work in self.works] + dois = [doi.replace("https://doi.org/", "") for doi in dois] + paper = Paper.objects.filter(doi__in=dois).first() + + authorships = paper.authorships.all() + self.assertGreater(len(authorships), 0) + + @patch.object(OpenAlex, "get_authors") + def create_authorship_institutions_when_processing_work(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) + + process_openalex_works(self.works) + + dois = [work.get("doi") for work in self.works] + dois = [doi.replace("https://doi.org/", "") for doi in dois] + paper = Paper.objects.filter(doi__in=dois).first() + + authorship = paper.authorships.first() + institutions = authorship.institutions.all() + self.assertGreater(len(institutions), 0) + + @patch.object(OpenAlex, "get_authors") + def test_add_orcid_to_author_when_processing_work(self, mock_get_authors): + # Note: In actuality orcid value could be null but the payload in this + # test has an orcid value in order to test if orcid is set properly when exists in payload + + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) + + open_alex = OpenAlex() + open_alex.get_authors() + + process_openalex_works(self.works) + author = Author.objects.filter(orcid_id__isnull=False).first() + self.assertIsNotNone(author.orcid_id) + + @patch.object(OpenAlex, "get_authors") + def test_author_summary_stats_are_set(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) + + open_alex = OpenAlex() + open_alex.get_authors() + + process_openalex_works(self.works) + author = Author.objects.filter( + openalex_ids__contains=[mock_data["results"][0]["id"]] + ).first() + + self.assertGreater(author.h_index, 0) + self.assertGreater(author.two_year_mean_citedness, 0) + self.assertGreater(author.i10_index, 0) + + @patch.object(OpenAlex, "get_authors") + def test_create_coauthor_relationship(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) + + open_alex = OpenAlex() + open_alex.get_authors() + + process_openalex_works(self.works) + author = Author.objects.filter( + openalex_ids__contains=[mock_data["results"][0]["id"]] + ).first() + + self.assertGreater(author.coauthors.count(), 0) + + @patch.object(OpenAlex, "get_authors") + def test_create_contribution_activity(self, mock_get_authors): + with open("./paper/tests/openalex_authors.json", "r") as file: + mock_data = json.load(file) + mock_get_authors.return_value = (mock_data["results"], None) + + process_openalex_works(self.works) + author = Author.objects.filter( + openalex_ids__contains=[mock_data["results"][0]["id"]] + ).first() + + self.assertGreater(len(author.contribution_summaries.all()), 0) diff --git a/src/researchhub/urls.py b/src/researchhub/urls.py index de285bb9e..a2130583a 100644 --- a/src/researchhub/urls.py +++ b/src/researchhub/urls.py @@ -45,7 +45,7 @@ from researchhub.settings import INSTALLED_APPS, USE_DEBUG_TOOLBAR from researchhub_comment.views.rh_comment_view import RhCommentViewSet from review.views.review_view import ReviewViewSet -from user.views import editor_views +from user.views import author_views, editor_views router = routers.DefaultRouter() @@ -81,7 +81,7 @@ basename="paper_submission", ) -router.register(r"author", user.views.AuthorViewSet, basename="author") +router.register(r"author", author_views.AuthorViewSet, basename="author") router.register(r"hub", hub.views.HubViewSet, basename="hub") diff --git a/src/researchhub_document/management/commands/load_works_from_openalex.py b/src/researchhub_document/management/commands/load_works_from_openalex.py index 5a8293cb2..f1cc9e21a 100644 --- a/src/researchhub_document/management/commands/load_works_from_openalex.py +++ b/src/researchhub_document/management/commands/load_works_from_openalex.py @@ -1,8 +1,10 @@ from django.core.management.base import BaseCommand +from django.utils import timezone from paper.openalex_util import process_openalex_works from paper.related_models.paper_model import Paper from topic.models import Topic +from user.related_models.author_model import Author from utils.openalex import OpenAlex # To pull papers from bioRxiv use source param: @@ -46,6 +48,18 @@ def add_arguments(self, parser): type=str, help="The paper respository source to pull from", ) + parser.add_argument( + "--openalex_id", + default=None, + type=str, + help="The OpenAlex ID to pull", + ) + parser.add_argument( + "--openalex_author_id", + default=None, + type=str, + help="The OpenAlex Author ID to pull", + ) parser.add_argument( "--mode", default="backfill", @@ -56,6 +70,8 @@ def add_arguments(self, parser): def handle(self, *args, **kwargs): start_id = kwargs["start_id"] to_id = kwargs["to_id"] + openalex_id = kwargs["openalex_id"] + openalex_author_id = kwargs["openalex_author_id"] mode = kwargs["mode"] source = kwargs["source"] batch_size = 100 @@ -90,8 +106,39 @@ def handle(self, *args, **kwargs): cursor = "*" page = 1 + openalex_ids = None + openalex_types = [ + "article", + "preprint", + "review", + ] + + if openalex_id: + print("Fetching single work with id: " + openalex_id) + work = OA.get_work( + openalex_id=openalex_id, + ) + + process_openalex_works([work]) + elif openalex_author_id: + print("Fetching full author works for author: " + openalex_author_id) + while cursor: print("Processing page " + str(page)) - works, cursor = OA.get_works(source_id=source, next_cursor=cursor) + works, cursor = OA.get_works( + source_id=source, + types=openalex_types, + next_cursor=cursor, + openalex_ids=openalex_ids, + openalex_author_id=openalex_author_id, + ) + process_openalex_works(works) page += 1 + + if openalex_author_id: + print("Finished fetching all works for author: " + openalex_author_id) + full_openalex_id = "https://openalex.org/" + openalex_author_id + author = Author.objects.get(openalex_ids__contains=[full_openalex_id]) + author.last_full_fetch_from_openalex = timezone.now() + author.save() diff --git a/src/user/migrations/0106_authorinstitution.py b/src/user/migrations/0106_authorinstitution.py new file mode 100644 index 000000000..5a5a16802 --- /dev/null +++ b/src/user/migrations/0106_authorinstitution.py @@ -0,0 +1,61 @@ +# Generated by Django 4.1 on 2024-05-17 20:27 + +import django.contrib.postgres.fields +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + dependencies = [ + ("institution", "0004_institution_openalex_created_date_and_more"), + ("user", "0105_remove_author_academic_verification_and_more"), + ] + + operations = [ + migrations.CreateModel( + name="AuthorInstitution", + fields=[ + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("created_date", models.DateTimeField(auto_now_add=True)), + ("updated_date", models.DateTimeField(auto_now=True)), + ( + "years", + django.contrib.postgres.fields.ArrayField( + base_field=models.IntegerField(), + blank=True, + default=list, + size=None, + ), + ), + ("is_primary", models.BooleanField(default=False)), + ( + "author", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="institutions", + to="user.author", + ), + ), + ( + "institution", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="author_institutions", + to="institution.institution", + ), + ), + ], + options={ + "unique_together": {("author", "institution")}, + }, + ), + ] diff --git a/src/user/migrations/0107_author_two_year_mean_citedness.py b/src/user/migrations/0107_author_two_year_mean_citedness.py new file mode 100644 index 000000000..c8a93051b --- /dev/null +++ b/src/user/migrations/0107_author_two_year_mean_citedness.py @@ -0,0 +1,18 @@ +# Generated by Django 4.1 on 2024-05-17 22:30 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0106_authorinstitution"), + ] + + operations = [ + migrations.AddField( + model_name="author", + name="two_year_mean_citedness", + field=models.FloatField(default=0), + ), + ] diff --git a/src/user/migrations/0108_delete_authorcitation.py b/src/user/migrations/0108_delete_authorcitation.py new file mode 100644 index 000000000..7333e07a4 --- /dev/null +++ b/src/user/migrations/0108_delete_authorcitation.py @@ -0,0 +1,16 @@ +# Generated by Django 4.1 on 2024-05-17 22:51 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0107_author_two_year_mean_citedness"), + ] + + operations = [ + migrations.DeleteModel( + name="AuthorCitation", + ), + ] diff --git a/src/user/migrations/0109_coauthor.py b/src/user/migrations/0109_coauthor.py new file mode 100644 index 000000000..0c37c9635 --- /dev/null +++ b/src/user/migrations/0109_coauthor.py @@ -0,0 +1,56 @@ +# Generated by Django 4.1 on 2024-05-21 00:05 + +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + dependencies = [ + ("paper", "0126_authorship_delete_workauthorship"), + ("user", "0108_delete_authorcitation"), + ] + + operations = [ + migrations.CreateModel( + name="CoAuthor", + fields=[ + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "author", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="coauthor_relationships", + to="user.author", + ), + ), + ( + "coauthor", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="coauthored_with", + to="user.author", + ), + ), + ( + "paper", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="coauthorships", + to="paper.paper", + ), + ), + ], + options={ + "unique_together": {("author", "coauthor", "paper")}, + }, + ), + ] diff --git a/src/user/migrations/0110_alter_coauthor_author.py b/src/user/migrations/0110_alter_coauthor_author.py new file mode 100644 index 000000000..4f48deef1 --- /dev/null +++ b/src/user/migrations/0110_alter_coauthor_author.py @@ -0,0 +1,23 @@ +# Generated by Django 4.1 on 2024-05-21 00:39 + +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0109_coauthor"), + ] + + operations = [ + migrations.AlterField( + model_name="coauthor", + name="author", + field=models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="coauthors", + to="user.author", + ), + ), + ] diff --git a/src/user/migrations/0111_alter_authorinstitution_unique_together.py b/src/user/migrations/0111_alter_authorinstitution_unique_together.py new file mode 100644 index 000000000..4f32e67d5 --- /dev/null +++ b/src/user/migrations/0111_alter_authorinstitution_unique_together.py @@ -0,0 +1,17 @@ +# Generated by Django 4.1 on 2024-05-21 19:45 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0110_alter_coauthor_author"), + ] + + operations = [ + migrations.AlterUniqueTogether( + name="authorinstitution", + unique_together=set(), + ), + ] diff --git a/src/user/migrations/0112_alter_author_orcid_id.py b/src/user/migrations/0112_alter_author_orcid_id.py new file mode 100644 index 000000000..f4b40c168 --- /dev/null +++ b/src/user/migrations/0112_alter_author_orcid_id.py @@ -0,0 +1,20 @@ +# Generated by Django 4.1 on 2024-05-21 20:02 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0111_alter_authorinstitution_unique_together"), + ] + + operations = [ + migrations.AlterField( + model_name="author", + name="orcid_id", + field=models.CharField( + blank=True, default=None, max_length=1024, null=True + ), + ), + ] diff --git a/src/user/migrations/0113_authorcontributionsummary.py b/src/user/migrations/0113_authorcontributionsummary.py new file mode 100644 index 000000000..3e1e7764a --- /dev/null +++ b/src/user/migrations/0113_authorcontributionsummary.py @@ -0,0 +1,52 @@ +# Generated by Django 4.1 on 2024-05-22 14:14 + +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0112_alter_author_orcid_id"), + ] + + operations = [ + migrations.CreateModel( + name="AuthorContributionSummary", + fields=[ + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "source", + models.CharField( + choices=[ + ("OPENALEX", "OpenAlex"), + ("RESEARCHHUB", "ResearchHub"), + ], + max_length=20, + ), + ), + ("works_count", models.IntegerField(blank=True, null=True)), + ("citation_count", models.IntegerField(blank=True, null=True)), + ("year", models.IntegerField()), + ( + "author", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="contribution_summaries", + to="user.author", + ), + ), + ], + options={ + "unique_together": {("source", "author", "year")}, + }, + ), + ] diff --git a/src/user/migrations/0113_remove_authorinstitution_is_primary.py b/src/user/migrations/0113_remove_authorinstitution_is_primary.py new file mode 100644 index 000000000..291be3951 --- /dev/null +++ b/src/user/migrations/0113_remove_authorinstitution_is_primary.py @@ -0,0 +1,17 @@ +# Generated by Django 4.1 on 2024-05-22 20:35 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0112_alter_author_orcid_id"), + ] + + operations = [ + migrations.RemoveField( + model_name="authorinstitution", + name="is_primary", + ), + ] diff --git a/src/user/migrations/0114_merge_20240523_0259.py b/src/user/migrations/0114_merge_20240523_0259.py new file mode 100644 index 000000000..b7bc8ebad --- /dev/null +++ b/src/user/migrations/0114_merge_20240523_0259.py @@ -0,0 +1,13 @@ +# Generated by Django 4.1 on 2024-05-23 02:59 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0113_authorcontributionsummary"), + ("user", "0113_remove_authorinstitution_is_primary"), + ] + + operations = [] diff --git a/src/user/migrations/0114_merge_20240524_0059.py b/src/user/migrations/0114_merge_20240524_0059.py new file mode 100644 index 000000000..72a8aae22 --- /dev/null +++ b/src/user/migrations/0114_merge_20240524_0059.py @@ -0,0 +1,13 @@ +# Generated by Django 4.1 on 2024-05-24 00:59 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0113_authorcontributionsummary"), + ("user", "0113_remove_authorinstitution_is_primary"), + ] + + operations = [] diff --git a/src/user/migrations/0115_alter_authorcontributionsummary_citation_count_and_more.py b/src/user/migrations/0115_alter_authorcontributionsummary_citation_count_and_more.py new file mode 100644 index 000000000..715e1422c --- /dev/null +++ b/src/user/migrations/0115_alter_authorcontributionsummary_citation_count_and_more.py @@ -0,0 +1,23 @@ +# Generated by Django 4.1 on 2024-05-23 03:00 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0114_merge_20240523_0259"), + ] + + operations = [ + migrations.AlterField( + model_name="authorcontributionsummary", + name="citation_count", + field=models.IntegerField(blank=True, default=0), + ), + migrations.AlterField( + model_name="authorcontributionsummary", + name="works_count", + field=models.IntegerField(blank=True, default=0), + ), + ] diff --git a/src/user/migrations/0115_author_created_source_and_more.py b/src/user/migrations/0115_author_created_source_and_more.py new file mode 100644 index 000000000..48e3b8b44 --- /dev/null +++ b/src/user/migrations/0115_author_created_source_and_more.py @@ -0,0 +1,27 @@ +# Generated by Django 4.1 on 2024-05-24 01:07 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0114_merge_20240524_0059"), + ] + + operations = [ + migrations.AddField( + model_name="author", + name="created_source", + field=models.CharField( + choices=[("OPENALEX", "OpenAlex"), ("RESEARCHHUB", "ResearchHub")], + default="RESEARCHHUB", + max_length=20, + ), + ), + migrations.AddField( + model_name="author", + name="last_full_fetch_from_openalex", + field=models.DateTimeField(blank=True, null=True), + ), + ] diff --git a/src/user/migrations/0116_merge_20240524_2253.py b/src/user/migrations/0116_merge_20240524_2253.py new file mode 100644 index 000000000..7e65244d2 --- /dev/null +++ b/src/user/migrations/0116_merge_20240524_2253.py @@ -0,0 +1,13 @@ +# Generated by Django 4.1 on 2024-05-24 22:53 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ("user", "0115_alter_authorcontributionsummary_citation_count_and_more"), + ("user", "0115_author_created_source_and_more"), + ] + + operations = [] diff --git a/src/user/models.py b/src/user/models.py index 4c682bb91..6787abee5 100644 --- a/src/user/models.py +++ b/src/user/models.py @@ -1,5 +1,4 @@ from .related_models.action_model import Action -from .related_models.author_citation_model import AuthorCitation from .related_models.author_model import Author from .related_models.follow_model import Follow from .related_models.gatekeeper_model import Gatekeeper @@ -13,7 +12,6 @@ migratables = ( Action, Author, - AuthorCitation, Follow, Major, ProfileImageStorage, diff --git a/src/user/related_models/author_citation_model.py b/src/user/related_models/author_citation_model.py deleted file mode 100644 index ddabcba36..000000000 --- a/src/user/related_models/author_citation_model.py +++ /dev/null @@ -1,12 +0,0 @@ -from django.db import models - - -class AuthorCitation(models.Model): - author = models.ForeignKey( - "user.Author", related_name="citations", on_delete=models.CASCADE - ) - citation_count = models.IntegerField(default=0) - citation_name = models.CharField(max_length=256) - cited_by_url = models.URLField(max_length=256, null=True) - publish_year = models.CharField(max_length=4) - title = models.CharField(max_length=256) diff --git a/src/user/related_models/author_contribution_summary_model.py b/src/user/related_models/author_contribution_summary_model.py new file mode 100644 index 000000000..43e6808aa --- /dev/null +++ b/src/user/related_models/author_contribution_summary_model.py @@ -0,0 +1,22 @@ +from django.db import models + + +class AuthorContributionSummary(models.Model): + SOURCE_OPENALEX = "OPENALEX" + SOURCE_RESEARCHHUB = "RESEARCHHUB" + SOURCE_CHOICES = [ + (SOURCE_OPENALEX, "OpenAlex"), + (SOURCE_RESEARCHHUB, "ResearchHub"), + ] + source = models.CharField( + max_length=20, null=False, blank=False, choices=SOURCE_CHOICES + ) + author = models.ForeignKey( + "user.Author", on_delete=models.CASCADE, related_name="contribution_summaries" + ) + works_count = models.IntegerField(null=False, blank=True, default=0) + citation_count = models.IntegerField(null=False, blank=True, default=0) + year = models.IntegerField(null=False, blank=False) + + class Meta: + unique_together = ("source", "author", "year") diff --git a/src/user/related_models/author_institution.py b/src/user/related_models/author_institution.py new file mode 100644 index 000000000..d0edbea52 --- /dev/null +++ b/src/user/related_models/author_institution.py @@ -0,0 +1,20 @@ +from django.contrib.postgres.fields import ArrayField +from django.db import models + +from utils.models import DefaultModel + + +class AuthorInstitution(DefaultModel): + author = models.ForeignKey( + "user.Author", + on_delete=models.CASCADE, + related_name="institutions", + ) + + institution = models.ForeignKey( + "institution.Institution", + on_delete=models.CASCADE, + related_name="author_institutions", + ) + + years = ArrayField(models.IntegerField(), blank=True, default=list) diff --git a/src/user/related_models/author_model.py b/src/user/related_models/author_model.py index 6f44ed307..12916401f 100644 --- a/src/user/related_models/author_model.py +++ b/src/user/related_models/author_model.py @@ -9,6 +9,11 @@ from paper.utils import PAPER_SCORE_Q_ANNOTATION from purchase.related_models.purchase_model import Purchase from researchhub_case.constants.case_constants import APPROVED +from user.related_models.author_contribution_summary_model import ( + AuthorContributionSummary, +) +from user.related_models.author_institution import AuthorInstitution +from user.related_models.coauthor_model import CoAuthor from user.related_models.profile_image_storage import ProfileImageStorage from user.related_models.school_model import University from user.related_models.user_model import User @@ -17,6 +22,12 @@ class Author(models.Model): + SOURCE_OPENALEX = "OPENALEX" + SOURCE_RESEARCHHUB = "RESEARCHHUB" + SOURCE_CHOICES = [ + (SOURCE_OPENALEX, "OpenAlex"), + (SOURCE_RESEARCHHUB, "ResearchHub"), + ] user = models.OneToOneField( User, related_name="author_profile", @@ -44,7 +55,7 @@ class Author(models.Model): University, on_delete=models.SET_NULL, null=True, blank=True ) orcid_id = models.CharField( - max_length=1024, default=None, null=True, blank=True, unique=True + max_length=1024, default=None, null=True, blank=True, unique=False ) openalex_ids = ArrayField( models.CharField( @@ -71,6 +82,21 @@ class Author(models.Model): max_length=20, ) + # Indicates whether the user was created through the RH platform or through another source such as OpenAlex + created_source = models.CharField( + max_length=20, + null=False, + blank=False, + choices=SOURCE_CHOICES, + default=SOURCE_RESEARCHHUB, + ) + + # Indicates the last time we did a full fetch from OpenAlex which includes all the works + last_full_fetch_from_openalex = models.DateTimeField(null=True, blank=True) + + # AKA Impact Factor. Derived from OpenAlex: https://en.wikipedia.org/wiki/Impact_factor + two_year_mean_citedness = models.FloatField(default=0) + def __str__(self): university = self.university if university is None: diff --git a/src/user/related_models/coauthor_model.py b/src/user/related_models/coauthor_model.py new file mode 100644 index 000000000..14b3f0b88 --- /dev/null +++ b/src/user/related_models/coauthor_model.py @@ -0,0 +1,16 @@ +from django.db import models + + +class CoAuthor(models.Model): + author = models.ForeignKey( + "user.Author", related_name="coauthors", on_delete=models.CASCADE + ) + coauthor = models.ForeignKey( + "user.Author", related_name="coauthored_with", on_delete=models.CASCADE + ) + paper = models.ForeignKey( + "paper.Paper", related_name="coauthorships", on_delete=models.CASCADE + ) + + class Meta: + unique_together = ("author", "coauthor", "paper") diff --git a/src/user/serializers.py b/src/user/serializers.py index 6e1ce3c31..3ed96a278 100644 --- a/src/user/serializers.py +++ b/src/user/serializers.py @@ -2,6 +2,7 @@ import dj_rest_auth.registration.serializers as rest_auth_serializers from django.contrib.contenttypes.models import ContentType +from django.db import models from rest_framework.serializers import ( CharField, IntegerField, @@ -19,6 +20,7 @@ from hub.models import Hub from hub.serializers import DynamicHubSerializer, HubSerializer, SimpleHubSerializer from hypothesis.models import Hypothesis +from institution.serializers import DynamicInstitutionSerializer from paper.models import Paper, PaperSubmission from purchase.models import Purchase from reputation.models import Bounty, Contribution, Withdrawal @@ -39,6 +41,11 @@ UserApiToken, Verdict, ) +from user.related_models.author_contribution_summary_model import ( + AuthorContributionSummary, +) +from user.related_models.author_institution import AuthorInstitution +from user.related_models.coauthor_model import CoAuthor from user.related_models.gatekeeper_model import Gatekeeper from utils import sentry @@ -218,6 +225,8 @@ class Meta: class DynamicAuthorSerializer(DynamicModelFieldSerializer): + count = IntegerField(read_only=True) + class Meta: model = Author fields = "__all__" @@ -1001,3 +1010,132 @@ def get_flag(self, verdict): def get_flagged_content_name(self, verdict): return verdict.flag.content_type.name + + +class DynamicAuthorInstitutionSerializer(DynamicModelFieldSerializer): + institution = SerializerMethodField() + + class Meta: + model = AuthorInstitution + fields = "__all__" + + def get_institution(self, author_institution): + context = self.context + _context_fields = context.get("author_institution::get_institution", {}) + + institution = author_institution.institution + serializer = DynamicInstitutionSerializer( + institution, context=context, **_context_fields + ) + return serializer.data + + +class DynamicCoAuthorSerializer(DynamicModelFieldSerializer): + coauthor = SerializerMethodField() + + class Meta: + model = CoAuthor + fields = "__all__" + + def get_coauthor(self, coauthor): + context = self.context + _context_fields = context.get("coauthor::get_coauthor", {}) + + serializer = DynamicAuthorSerializer( + coauthor.coauthor, context=context, **_context_fields + ) + return serializer.data + + +class DynamicAuthorProfileSerializer(DynamicModelFieldSerializer): + institutions = SerializerMethodField() + coauthors = SerializerMethodField() + activity_by_year = SerializerMethodField() + works_count = SerializerMethodField() + citation_count = SerializerMethodField() + summary_stats = SerializerMethodField() + + class Meta: + model = Author + fields = "__all__" + + def get_summary_stats(self, author): + from django.db.models import Sum + + citation_count = author.authored_papers.aggregate( + total_citations=Sum("citations") + )["total_citations"] + + return { + "works_count": author.authored_papers.count(), + "citation_count": citation_count, + "two_year_mean_citedness": author.two_year_mean_citedness, + } + + def get_activity_by_year(self, author): + context = self.context + _context_fields = context.get("author_profile::activity_by_year", {}) + + serializer = DynamicAuthorContributionSummarySerializer( + author.contribution_summaries.all(), + context=context, + many=True, + **_context_fields, + ) + return serializer.data + + def get_institutions(self, author): + context = self.context + _context_fields = context.get("author_profile::get_institutions", {}) + + serializer = DynamicAuthorInstitutionSerializer( + author.institutions, context=context, many=True, **_context_fields + ) + return serializer.data + + def get_coauthors(self, author): + from django.db.models import Count + + context = self.context + _context_fields = context.get("author_profile::get_coauthors", {}) + + coauthors = ( + CoAuthor.objects.filter(author=author) + .values( + "coauthor", + "coauthor__first_name", + "coauthor__last_name", + "coauthor__is_verified", + "coauthor__headline", + "coauthor__description", + ) + .annotate(count=Count("coauthor")) + .order_by("-count")[:10] + ) + + coauthor_data = [ + { + "id": co["coauthor"], + "first_name": co["coauthor__first_name"], + "last_name": co["coauthor__last_name"], + "is_verified": co["coauthor__is_verified"], + "headline": co["coauthor__headline"], + "description": co["coauthor__description"], + "count": co["count"], + } + for co in coauthors + ] + + serializer = DynamicAuthorSerializer( + coauthor_data, + context=context, + many=True, + **_context_fields, + ) + return serializer.data + + +class DynamicAuthorContributionSummarySerializer(DynamicModelFieldSerializer): + class Meta: + model = AuthorContributionSummary + fields = "__all__" diff --git a/src/user/views/__init__.py b/src/user/views/__init__.py index ae3412fb9..67d0b76e0 100644 --- a/src/user/views/__init__.py +++ b/src/user/views/__init__.py @@ -1,5 +1,6 @@ # flake8: noqa from user.views.audit_views import AuditViewSet +from user.views.author_views import AuthorViewSet from user.views.contribution_views import ContributionViewSet from user.views.editor_views import * from user.views.gatekeeper_view import GatekeeperViewSet diff --git a/src/user/views/author_views.py b/src/user/views/author_views.py new file mode 100644 index 000000000..3c41847ad --- /dev/null +++ b/src/user/views/author_views.py @@ -0,0 +1,980 @@ +import hmac +from datetime import datetime, timedelta +from hashlib import sha1 + +from allauth.account.models import EmailAddress +from django.contrib.contenttypes.models import ContentType +from django.core.cache import cache +from django.db import IntegrityError, models, transaction +from django.db.models import Exists, F, OuterRef, Q, Sum +from django.db.models.functions import Coalesce +from django.shortcuts import get_object_or_404 +from django.utils import timezone +from django.utils.decorators import method_decorator +from django.views.decorators.cache import cache_page +from django_filters.rest_framework import DjangoFilterBackend +from requests.exceptions import HTTPError +from rest_framework import status, viewsets +from rest_framework.decorators import action, api_view, permission_classes +from rest_framework.filters import OrderingFilter, SearchFilter +from rest_framework.permissions import ( + AllowAny, + IsAuthenticated, + IsAuthenticatedOrReadOnly, +) +from rest_framework.response import Response +from rest_framework.utils.urls import replace_query_param + +from discussion.models import Comment, Reply, Thread +from discussion.serializers import DynamicThreadSerializer +from hypothesis.related_models.hypothesis import Hypothesis +from paper.models import Paper +from paper.serializers import DynamicPaperSerializer +from paper.tasks import pull_openalex_author_works +from paper.utils import PAPER_SCORE_Q_ANNOTATION, get_cache_key +from paper.views import PaperViewSet +from reputation.models import Bounty, BountySolution, Contribution, Distribution +from reputation.serializers import ( + DynamicBountySerializer, + DynamicBountySolutionSerializer, + DynamicContributionSerializer, +) +from reputation.views import BountyViewSet +from researchhub.settings import ( + EMAIL_WHITELIST, + SIFT_MODERATION_WHITELIST, + SIFT_WEBHOOK_SECRET_KEY, +) +from researchhub_comment.models import RhCommentModel +from researchhub_document.related_models.researchhub_post_model import ResearchhubPost +from researchhub_document.serializers import DynamicPostSerializer +from review.models.review_model import Review +from user.filters import AuthorFilter, UserFilter +from user.models import Author, Follow, Major, University, User, UserApiToken +from user.permissions import ( + Censor, + DeleteAuthorPermission, + DeleteUserPermission, + HasVerificationPermission, + RequestorIsOwnUser, + UpdateAuthor, +) +from user.serializers import ( + AuthorEditableSerializer, + AuthorSerializer, + DynamicAuthorProfileSerializer, + DynamicUserSerializer, + MajorSerializer, + UniversitySerializer, + UserActions, + UserEditableSerializer, + UserSerializer, +) +from user.tasks import handle_spam_user_task, reinstate_user_task +from user.utils import calculate_show_referral, reset_latest_acitvity_cache +from utils.http import POST, RequestMethods +from utils.openalex import OpenAlex +from utils.permissions import CreateOrUpdateIfAllowed +from utils.sentry import log_error, log_info +from utils.throttles import THROTTLE_CLASSES + + +class AuthorViewSet(viewsets.ModelViewSet): + queryset = Author.objects.all() + serializer_class = AuthorSerializer + filter_backends = (SearchFilter, DjangoFilterBackend, OrderingFilter) + filter_class = AuthorFilter + search_fields = ("first_name", "last_name") + permission_classes = [ + (IsAuthenticatedOrReadOnly & UpdateAuthor & CreateOrUpdateIfAllowed) + | DeleteAuthorPermission + ] + throttle_classes = THROTTLE_CLASSES + + def create(self, request, *args, **kwargs): + """Override to use an editable serializer.""" + serializer = AuthorEditableSerializer(data=request.data) + serializer.is_valid(raise_exception=True) + self.perform_create(serializer) + headers = self.get_success_headers(serializer.data) + return Response( + serializer.data, status=status.HTTP_201_CREATED, headers=headers + ) + + def update(self, request, *args, **kwargs): + """Override to use an editable serializer.""" + partial = kwargs.pop("partial", False) + instance = self.get_object() + serializer = AuthorEditableSerializer( + instance, data=request.data, partial=partial + ) + serializer.is_valid(raise_exception=True) + self.perform_update(serializer) + + if getattr(instance, "_prefetched_objects_cache", None): + # If 'prefetch_related' has been applied to a queryset, we need to + # forcibly invalidate the prefetch cache on the instance. + instance._prefetched_objects_cache = {} + + return Response(serializer.data) + + @action(detail=True, methods=["get"], permission_classes=[AllowAny]) + def profile(self, request, pk=None): + author = self.get_object() + serializer = DynamicAuthorProfileSerializer( + author, + context={ + "author_institution::get_institution": { + "_include_fields": [ + "id", + "display_name", + "region", + "city", + "latitude", + "longitude", + "image_url", + "image_thumbnail_url", + ] + }, + "author_profile::get_institutions": { + "_include_fields": [ + "id", + "years", + "is_primary", + "institution", + ] + }, + "author_profile::activity_by_year": { + "_include_fields": [ + "year", + "works_count", + "citation_count", + ] + }, + "author_profile::get_coauthors": { + "_include_fields": [ + "id", + "first_name", + "last_name", + "count", + "is_verified", + "profile_image", + "headline", + "description", + ] + }, + }, + _include_fields=( + "id", + "openalex_ids", + "first_name", + "last_name", + "description", + "headline", + "profile_image", + "orcid_id", + "h_index", + "i10_index", + "google_scholar", + "linkedin", + "twitter", + "institutions", + "created_date", + "country_code", + "coauthors", + "summary_stats", + "activity_by_year", + ), + ) + return Response(serializer.data, status=200) + + @action( + detail=True, + methods=["get"], + ) + def get_authored_papers(self, request, pk=None): + author = self.get_object() + prefetch_lookups = PaperViewSet.prefetch_lookups(self) + authored_papers = ( + author.authored_papers.filter(is_removed=False) + .prefetch_related( + *prefetch_lookups, + ) + .annotate(paper_score=PAPER_SCORE_Q_ANNOTATION) + .order_by("-paper_score") + ) + context = self._get_authored_papers_context() + page = self.paginate_queryset(authored_papers) + serializer = DynamicPaperSerializer( + page, + _include_fields=[ + "id", + "abstract", + "authors", + "boost_amount", + "file", + "first_preview", + "hubs", + "paper_title", + "score", + "title", + "uploaded_by", + "uploaded_date", + "url", + "paper_publish_date", + "slug", + "created_date", + ], + many=True, + context=context, + ) + response = self.get_paginated_response(serializer.data) + return response + + def _get_authored_papers_context(self): + context = { + "pap_dps_get_authors": { + "_include_fields": [ + "id", + "first_name", + "last_name", + "profile_image", + ] + }, + "pap_dps_get_uploaded_by": { + "_include_fields": [ + "id", + "author_profile", + ] + }, + "pap_dps_get_first_preview": { + "_include_fields": [ + "file", + ] + }, + "pap_dps_get_hubs": { + "_include_fields": ( + "id", + "slug", + "name", + ) + }, + "usr_dus_get_author_profile": { + "_include_fields": ["id", "first_name", "last_name", "profile_image"] + }, + "doc_duds_get_hubs": { + "_include_fields": [ + "id", + "name", + "slug", + "hub_image", + ] + }, + } + return context + + def _get_contribution_context(self, filter_by_user_id): + context = { + "request": self.request, + "_config": { + "filter_by_user_id": filter_by_user_id, + }, + "doc_dps_get_created_by": { + "_include_fields": [ + "id", + "author_profile", + ] + }, + "doc_duds_get_created_by": { + "_include_fields": [ + "id", + "author_profile", + ] + }, + "doc_dps_get_hubs": { + "_include_fields": [ + "name", + "slug", + ] + }, + "pap_dps_get_uploaded_by": { + "_include_fields": [ + "id", + "author_profile", + ] + }, + "dis_dts_get_created_by": { + "_include_fields": [ + "id", + "author_profile", + ] + }, + "dis_dts_get_review": { + "_include_fields": [ + "id", + "score", + ] + }, + "dis_dcs_get_created_by": { + "_include_fields": [ + "author_profile", + "id", + ] + }, + "dis_drs_get_created_by": { + "_include_fields": [ + "author_profile", + "id", + ] + }, + "pap_dps_get_user_vote": { + "_include_fields": [ + "id", + "created_by", + "created_date", + "vote_type", + ] + }, + "pap_dps_get_hubs": { + "_include_fields": [ + "name", + "slug", + ] + }, + "pap_dpvs_paper": {"_exclude_fields": "__all__"}, + "doc_dps_get_user_vote": { + "_include_fields": [ + "id", + "content_type", + "created_by", + "created_date", + "vote_type", + "item", + ] + }, + "dis_drs_get_user_vote": { + "_include_fields": [ + "id", + "content_type", + "created_by", + "created_date", + "vote_type", + "item", + ] + }, + "dis_dcs_get_user_vote": { + "_include_fields": [ + "id", + "content_type", + "created_by", + "created_date", + "vote_type", + "item", + ] + }, + "dis_dts_get_user_vote": { + "_include_fields": [ + "id", + "content_type", + "created_by", + "created_date", + "vote_type", + "item", + ] + }, + "dis_dts_get_comments": { + "_include_fields": [ + "created_by", + "created_date", + "updated_date", + "created_location", + "external_metadata", + "id", + "is_created_by_editor", + "is_public", + "is_removed", + "paper_id", + "parent", + "plain_text", + "promoted", + "replies", + "reply_count", + "score", + "source", + "text", + "thread_id", + "user_flag", + "user_vote", + "was_edited", + ] + }, + "dis_dcs_get_replies": { + "_include_fields": [ + "created_by", + "created_location", + "id", + "is_created_by_editor", + "is_public", + "is_removed", + "paper_id", + "parent", + "plain_text", + "promoted", + "score", + "text", + "thread_id", + "user_flag", + "user_vote", + "created_date", + "updated_date", + ] + }, + "doc_duds_get_documents": { + "_include_fields": [ + "promoted", + "abstract", + "aggregate_citation_consensus", + "created_by", + "created_date", + "hot_score", + "hubs", + "id", + "discussion_count", + "paper_title", + "preview_img", + "renderable_text", + "score", + "slug", + "title", + "uploaded_by", + "uploaded_date", + "user_vote", + ] + }, + "doc_duds_get_bounties": {"_include_fields": ["id"]}, + "doc_duds_get_document_filter": { + "_include_fields": [ + "answered", + "bounty_open", + "bounty_total_amount", + ] + }, + "rep_dcs_get_author": { + "_include_fields": [ + "id", + "first_name", + "last_name", + "profile_image", + ] + }, + "rep_dcs_get_unified_document": { + "_include_fields": [ + "id", + "document_type", + "documents", + "hubs", + "document_filter", + ] + }, + "rep_dcs_get_source": { + "_include_fields": [ + "amount", + "citation", + "comment_count", + "comment_content_json", + # 02-18-24 Kobe: Temporarily commenting this out as it leads to a fatal error. + # I'm not sure this key is necessary for the client. Only time will tell + # "children", + "content_type", + "created_by", + "created_date", + "created_location", + "discussion_type", + "document_meta", + "external_metadata", + "hypothesis", + "id", + "is_public", + "is_removed", + "paper_slug", + "paper_title", + "paper", + "plain_text", + "post_slug", + "post", + "promoted", + "replies", + "review", + "score", + "slug", + "source", + "text", + "title", + "user_flag", + "user_vote", + "vote", + "bet_amount", + ] + }, + "rep_dbs_get_item": { + "_include_fields": [ + "created_by", + "created_date", + "updated_date", + "created_location", + "external_metadata", + "id", + "is_created_by_editor", + "is_public", + "is_removed", + "paper_id", + "parent", + "plain_text", + "promoted", + "replies", + "reply_count", + "score", + "source", + "text", + "thread_id", + "paper", + "post", + "awarded_bounty_amount", + "unified_document", + "user_flag", + "user_vote", + "was_edited", + ] + }, + "rep_dbss_get_item": { + "_include_fields": [ + "created_by", + "created_date", + "updated_date", + "created_location", + "external_metadata", + "id", + "is_created_by_editor", + "is_public", + "is_removed", + "paper_id", + "parent", + "plain_text", + "promoted", + "replies", + "reply_count", + "score", + "source", + "text", + "awarded_bounty_amount", + "thread_id", + "user_flag", + "user_vote", + "was_edited", + ] + }, + "rep_dbs_get_created_by": {"_include_fields": ["author_profile", "id"]}, + "dis_dts_get_bounties": { + "_include_fields": [ + "amount", + "created_by", + ] + }, + "dis_dts_get_paper": { + "_include_fields": [ + "id", + "slug", + ] + }, + "dis_dts_get_post": { + "_include_fields": [ + "id", + "slug", + ] + }, + "doc_duds_get_hubs": { + "_include_fields": [ + "name", + "slug", + ] + }, + "hyp_dhs_get_hubs": { + "_include_fields": [ + "name", + "slug", + ] + }, + "hyp_dhs_get_created_by": { + "_include_fields": [ + "author_profile", + "id", + ] + }, + "rhc_dcs_get_created_by": { + "_include_fields": [ + "first_name", + "last_name", + "author_profile", + ] + }, + "rhc_dcs_get_children": { + "_exclude_fields": [ + "thread", + "comment_content_src", + "promoted", + "user_endorsement", + "user_flag", + "purchases", + ] + }, + "rhc_dcs_get_purchases": { + "_include_fields": [ + "amount", + "user", + ] + }, + "rev_drs_get_created_by": { + "_include_fields": [ + "author_profile", + "id", + ] + }, + "pch_dps_get_user": { + "_include_fields": [ + "author_profile", + "id", + ] + }, + } + return context + + @action( + detail=True, + methods=["get"], + ) + def contributions(self, request, pk=None): + author = self.get_object() + + query_params = request.query_params + ordering = query_params.get("ordering", "-created_date") + asset_type = query_params.get("type", "overview") + contributions = self._get_author_contribution_queryset( + author.id, ordering, asset_type + ) + + page = self.paginate_queryset(contributions) + context = self._get_contribution_context(author.user_id) + serializer = DynamicContributionSerializer( + page, + _include_fields=[ + "contribution_type", + "created_date", + "id", + "source", + "created_by", + "unified_document", + "author", + ], + context=context, + many=True, + ) + data = serializer.data + response = self.get_paginated_response(data) + if asset_type == "bounty_offered": + total_bounty_amount = contributions.aggregate( + total_amount=Sum("bounty__amount") + ) + response.data["total_bounty_amount"] = total_bounty_amount.get( + "total_amount", 0 + ) + + return response + + def _get_author_comments(self, author_id): + author = self.get_object() + user = author.user + + if user: + user_threads = RhCommentModel.objects.filter(Q(created_by=user)) + return user_threads + return [] + + def _get_author_contribution_queryset(self, author_id, ordering, asset_type): + author_comments = self._get_author_comments(author_id) + rh_comment_content_type = ContentType.objects.get_for_model(RhCommentModel) + post_content_type = ContentType.objects.get_for_model(ResearchhubPost) + paper_content_type = ContentType.objects.get_for_model(Paper) + hypothesis_content_type = ContentType.objects.get_for_model(Hypothesis) + review_content_type = ContentType.objects.get_for_model(Review) + bounty_content_type = ContentType.objects.get_for_model(Bounty) + bounty_solution_content_type = ContentType.objects.get_for_model(BountySolution) + + types = asset_type.split(",") + + query = Q() + for asset_type in types: + if asset_type == "overview": + query |= Q( + Q( + unified_document__is_removed=False, + content_type=rh_comment_content_type, + # we filter by object_id instead of author_profile because + # sometimes there's contributions without a matching comment. + # this method ensures the comments exists. + object_id__in=author_comments, + contribution_type__in=[ + Contribution.COMMENTER, + ], + ) + | Q( + unified_document__is_removed=False, + user__author_profile=author_id, + content_type_id__in=[ + hypothesis_content_type, + paper_content_type, + post_content_type, + review_content_type, + ], + contribution_type__in=[ + Contribution.SUBMITTER, + Contribution.SUPPORTER, + ], + ) + ) + elif asset_type == "discussion": + query |= Q( + unified_document__is_removed=False, + user__author_profile=author_id, + content_type_id=post_content_type, + contribution_type__in=[Contribution.SUBMITTER], + ) + elif asset_type == "hypothesis": + query |= Q( + unified_document__is_removed=False, + user__author_profile=author_id, + content_type_id=hypothesis_content_type, + contribution_type__in=[Contribution.SUBMITTER], + ) + elif asset_type == "comment": + query |= Q( + unified_document__is_removed=False, + content_type=rh_comment_content_type, + # we filter by object_id instead of author_profile because + # sometimes there's contributions without a matching comment. + # this method ensures the comments exists. + object_id__in=author_comments, + contribution_type__in=[Contribution.COMMENTER], + ) + elif asset_type == "paper": + query |= Q( + unified_document__is_removed=False, + user__author_profile=author_id, + content_type_id=paper_content_type, + contribution_type__in=[Contribution.SUBMITTER], + ) + elif asset_type == "bounty_offered": + query |= Q( + unified_document__is_removed=False, + user__author_profile=author_id, + content_type_id=bounty_content_type, + contribution_type__in=[Contribution.BOUNTY_CREATED], + ) + elif asset_type == "bounty_earned": + query |= Q( + unified_document__is_removed=False, + user__author_profile=author_id, + content_type_id=bounty_solution_content_type, + contribution_type__in=[Contribution.BOUNTY_SOLUTION], + ) + else: + raise Exception("Unrecognized asset type: {}".format(asset_type)) + + qs = ( + Contribution.objects.filter(query) + .select_related( + "content_type", + "user", + "user__author_profile", + "unified_document", + ) + .order_by(ordering) + ) + + return qs + + @action( + detail=True, + methods=["get"], + ) + def get_user_discussions(self, request, pk=None): + author = self.get_object() + user = author.user + + if user: + user_discussions = user.thread_set.filter(is_removed=False).order_by("-id") + else: + user_discussions = self.queryset.none() + + page = self.paginate_queryset(user_discussions) + context = self._get_user_discussion_context() + serializer = DynamicThreadSerializer( + page, + _include_fields=[ + "id", + "comment_count", + "created_by", + "created_date", + "paper", + "post", + "score", + "text", + ], + many=True, + context=context, + ) + return self.get_paginated_response(serializer.data) + + def _get_user_discussion_context(self): + context = { + "dis_dts_get_created_by": { + "_include_fields": [ + "id", + "author_profile", + ] + }, + "dis_dts_get_paper": { + "_include_fields": [ + "id", + "slug", + ] + }, + "dis_dts_get_post": { + "_include_fields": [ + "id", + "slug", + ] + }, + "usr_dus_get_author_profile": { + "_include_fields": ["id", "first_name", "last_name", "profile_image"] + }, + } + return context + + @action( + detail=True, + methods=["get"], + ) + def get_user_contributions(self, request, pk=None): + author = self.get_object() + user = author.user + + if user: + prefetch_lookups = PaperViewSet.prefetch_lookups(self) + user_paper_uploads = user.papers.filter(is_removed=False).prefetch_related( + *prefetch_lookups + ) + else: + user_paper_uploads = self.queryset.none() + + context = self._get_user_contributions_context() + page = self.paginate_queryset(user_paper_uploads) + serializer = DynamicPaperSerializer( + page, + _include_fields=[ + "id", + "abstract", + "boost_amount", + "file", + "hubs", + "paper_title", + "score", + "title", + "slug", + "uploaded_by", + "uploaded_date", + ], + many=True, + context=context, + ) + response = self.get_paginated_response(serializer.data) + + return response + + def _get_user_contributions_context(self): + context = { + "pap_dps_get_uploaded_by": { + "_include_fields": [ + "id", + "author_profile", + ] + }, + "usr_dus_get_author_profile": { + "_include_fields": ["id", "first_name", "last_name", "profile_image"] + }, + "doc_duds_get_hubs": { + "_include_fields": [ + "id", + "name", + "slug", + "hub_image", + ] + }, + } + return context + + @action( + detail=True, + methods=["get"], + ) + def get_user_posts(self, request, pk=None): + author = self.get_object() + user = author.user + + if user: + user_posts = user.created_posts.all().prefetch_related( + "unified_document", "purchases" + ) + else: + user_posts = self.queryset.none() + + context = self._get_user_posts_context() + page = self.paginate_queryset(user_posts) + serializer = DynamicPostSerializer( + page, + _include_fields=[ + "id", + "created_by", + "hubs", + "boost_amount", + "renderable_text", + "score", + "slug", + "title", + ], + many=True, + context=context, + ) + response = self.get_paginated_response(serializer.data) + return response + + def _get_user_posts_context(self): + context = { + "doc_dps_get_created_by": { + "_include_fields": [ + "id", + "author_profile", + ] + }, + "usr_dus_get_author_profile": { + "_include_fields": ["id", "first_name", "last_name", "profile_image"] + }, + "doc_dps_get_hubs": { + "_include_fields": [ + "id", + "name", + "slug", + "hub_image", + ] + }, + } + return context diff --git a/src/user/views/user_views.py b/src/user/views/user_views.py index 75e533233..f0e15aa3d 100644 --- a/src/user/views/user_views.py +++ b/src/user/views/user_views.py @@ -914,834 +914,3 @@ class MajorViewSet(viewsets.ReadOnlyModelViewSet): filter_backends = (SearchFilter, DjangoFilterBackend, OrderingFilter) search_fields = ("major", "major_category") permission_classes = [AllowAny] - - -class AuthorViewSet(viewsets.ModelViewSet): - queryset = Author.objects.all() - serializer_class = AuthorSerializer - filter_backends = (SearchFilter, DjangoFilterBackend, OrderingFilter) - filter_class = AuthorFilter - search_fields = ("first_name", "last_name") - permission_classes = [ - (IsAuthenticatedOrReadOnly & UpdateAuthor & CreateOrUpdateIfAllowed) - | DeleteAuthorPermission - ] - throttle_classes = THROTTLE_CLASSES - - def create(self, request, *args, **kwargs): - """Override to use an editable serializer.""" - serializer = AuthorEditableSerializer(data=request.data) - serializer.is_valid(raise_exception=True) - self.perform_create(serializer) - headers = self.get_success_headers(serializer.data) - return Response( - serializer.data, status=status.HTTP_201_CREATED, headers=headers - ) - - def update(self, request, *args, **kwargs): - """Override to use an editable serializer.""" - partial = kwargs.pop("partial", False) - instance = self.get_object() - serializer = AuthorEditableSerializer( - instance, data=request.data, partial=partial - ) - serializer.is_valid(raise_exception=True) - self.perform_update(serializer) - - if getattr(instance, "_prefetched_objects_cache", None): - # If 'prefetch_related' has been applied to a queryset, we need to - # forcibly invalidate the prefetch cache on the instance. - instance._prefetched_objects_cache = {} - - return Response(serializer.data) - - @action( - detail=True, - methods=["get"], - ) - def get_authored_papers(self, request, pk=None): - author = self.get_object() - prefetch_lookups = PaperViewSet.prefetch_lookups(self) - authored_papers = ( - author.authored_papers.filter(is_removed=False) - .prefetch_related( - *prefetch_lookups, - ) - .annotate(paper_score=PAPER_SCORE_Q_ANNOTATION) - .order_by("-paper_score") - ) - context = self._get_authored_papers_context() - page = self.paginate_queryset(authored_papers) - serializer = DynamicPaperSerializer( - page, - _include_fields=[ - "id", - "abstract", - "authors", - "boost_amount", - "file", - "first_preview", - "hubs", - "paper_title", - "score", - "title", - "uploaded_by", - "uploaded_date", - "url", - "paper_publish_date", - "slug", - "created_date", - ], - many=True, - context=context, - ) - response = self.get_paginated_response(serializer.data) - return response - - def _get_authored_papers_context(self): - context = { - "pap_dps_get_authors": { - "_include_fields": [ - "id", - "first_name", - "last_name", - "profile_image", - ] - }, - "pap_dps_get_uploaded_by": { - "_include_fields": [ - "id", - "author_profile", - ] - }, - "pap_dps_get_first_preview": { - "_include_fields": [ - "file", - ] - }, - "pap_dps_get_hubs": { - "_include_fields": ( - "id", - "slug", - "name", - ) - }, - "usr_dus_get_author_profile": { - "_include_fields": ["id", "first_name", "last_name", "profile_image"] - }, - "doc_duds_get_hubs": { - "_include_fields": [ - "id", - "name", - "slug", - "hub_image", - ] - }, - } - return context - - def _get_contribution_context(self, filter_by_user_id): - context = { - "request": self.request, - "_config": { - "filter_by_user_id": filter_by_user_id, - }, - "doc_dps_get_created_by": { - "_include_fields": [ - "id", - "author_profile", - ] - }, - "doc_duds_get_created_by": { - "_include_fields": [ - "id", - "author_profile", - ] - }, - "doc_dps_get_hubs": { - "_include_fields": [ - "name", - "slug", - ] - }, - "pap_dps_get_uploaded_by": { - "_include_fields": [ - "id", - "author_profile", - ] - }, - "dis_dts_get_created_by": { - "_include_fields": [ - "id", - "author_profile", - ] - }, - "dis_dts_get_review": { - "_include_fields": [ - "id", - "score", - ] - }, - "dis_dcs_get_created_by": { - "_include_fields": [ - "author_profile", - "id", - ] - }, - "dis_drs_get_created_by": { - "_include_fields": [ - "author_profile", - "id", - ] - }, - "pap_dps_get_user_vote": { - "_include_fields": [ - "id", - "created_by", - "created_date", - "vote_type", - ] - }, - "pap_dps_get_hubs": { - "_include_fields": [ - "name", - "slug", - ] - }, - "pap_dpvs_paper": {"_exclude_fields": "__all__"}, - "doc_dps_get_user_vote": { - "_include_fields": [ - "id", - "content_type", - "created_by", - "created_date", - "vote_type", - "item", - ] - }, - "dis_drs_get_user_vote": { - "_include_fields": [ - "id", - "content_type", - "created_by", - "created_date", - "vote_type", - "item", - ] - }, - "dis_dcs_get_user_vote": { - "_include_fields": [ - "id", - "content_type", - "created_by", - "created_date", - "vote_type", - "item", - ] - }, - "dis_dts_get_user_vote": { - "_include_fields": [ - "id", - "content_type", - "created_by", - "created_date", - "vote_type", - "item", - ] - }, - "dis_dts_get_comments": { - "_include_fields": [ - "created_by", - "created_date", - "updated_date", - "created_location", - "external_metadata", - "id", - "is_created_by_editor", - "is_public", - "is_removed", - "paper_id", - "parent", - "plain_text", - "promoted", - "replies", - "reply_count", - "score", - "source", - "text", - "thread_id", - "user_flag", - "user_vote", - "was_edited", - ] - }, - "dis_dcs_get_replies": { - "_include_fields": [ - "created_by", - "created_location", - "id", - "is_created_by_editor", - "is_public", - "is_removed", - "paper_id", - "parent", - "plain_text", - "promoted", - "score", - "text", - "thread_id", - "user_flag", - "user_vote", - "created_date", - "updated_date", - ] - }, - "doc_duds_get_documents": { - "_include_fields": [ - "promoted", - "abstract", - "aggregate_citation_consensus", - "created_by", - "created_date", - "hot_score", - "hubs", - "id", - "discussion_count", - "paper_title", - "preview_img", - "renderable_text", - "score", - "slug", - "title", - "uploaded_by", - "uploaded_date", - "user_vote", - ] - }, - "doc_duds_get_bounties": {"_include_fields": ["id"]}, - "doc_duds_get_document_filter": { - "_include_fields": [ - "answered", - "bounty_open", - "bounty_total_amount", - ] - }, - "rep_dcs_get_author": { - "_include_fields": [ - "id", - "first_name", - "last_name", - "profile_image", - ] - }, - "rep_dcs_get_unified_document": { - "_include_fields": [ - "id", - "document_type", - "documents", - "hubs", - "document_filter", - ] - }, - "rep_dcs_get_source": { - "_include_fields": [ - "amount", - "citation", - "comment_count", - "comment_content_json", - # 02-18-24 Kobe: Temporarily commenting this out as it leads to a fatal error. - # I'm not sure this key is necessary for the client. Only time will tell - # "children", - "content_type", - "created_by", - "created_date", - "created_location", - "discussion_type", - "document_meta", - "external_metadata", - "hypothesis", - "id", - "is_public", - "is_removed", - "paper_slug", - "paper_title", - "paper", - "plain_text", - "post_slug", - "post", - "promoted", - "replies", - "review", - "score", - "slug", - "source", - "text", - "title", - "user_flag", - "user_vote", - "vote", - "bet_amount", - ] - }, - "rep_dbs_get_item": { - "_include_fields": [ - "created_by", - "created_date", - "updated_date", - "created_location", - "external_metadata", - "id", - "is_created_by_editor", - "is_public", - "is_removed", - "paper_id", - "parent", - "plain_text", - "promoted", - "replies", - "reply_count", - "score", - "source", - "text", - "thread_id", - "paper", - "post", - "awarded_bounty_amount", - "unified_document", - "user_flag", - "user_vote", - "was_edited", - ] - }, - "rep_dbss_get_item": { - "_include_fields": [ - "created_by", - "created_date", - "updated_date", - "created_location", - "external_metadata", - "id", - "is_created_by_editor", - "is_public", - "is_removed", - "paper_id", - "parent", - "plain_text", - "promoted", - "replies", - "reply_count", - "score", - "source", - "text", - "awarded_bounty_amount", - "thread_id", - "user_flag", - "user_vote", - "was_edited", - ] - }, - "rep_dbs_get_created_by": {"_include_fields": ["author_profile", "id"]}, - "dis_dts_get_bounties": { - "_include_fields": [ - "amount", - "created_by", - ] - }, - "dis_dts_get_paper": { - "_include_fields": [ - "id", - "slug", - ] - }, - "dis_dts_get_post": { - "_include_fields": [ - "id", - "slug", - ] - }, - "doc_duds_get_hubs": { - "_include_fields": [ - "name", - "slug", - ] - }, - "hyp_dhs_get_hubs": { - "_include_fields": [ - "name", - "slug", - ] - }, - "hyp_dhs_get_created_by": { - "_include_fields": [ - "author_profile", - "id", - ] - }, - "rhc_dcs_get_created_by": { - "_include_fields": [ - "first_name", - "last_name", - "author_profile", - ] - }, - "rhc_dcs_get_children": { - "_exclude_fields": [ - "thread", - "comment_content_src", - "promoted", - "user_endorsement", - "user_flag", - "purchases", - ] - }, - "rhc_dcs_get_purchases": { - "_include_fields": [ - "amount", - "user", - ] - }, - "rev_drs_get_created_by": { - "_include_fields": [ - "author_profile", - "id", - ] - }, - "pch_dps_get_user": { - "_include_fields": [ - "author_profile", - "id", - ] - }, - } - return context - - @action( - detail=True, - methods=["get"], - ) - def contributions(self, request, pk=None): - author = self.get_object() - - query_params = request.query_params - ordering = query_params.get("ordering", "-created_date") - asset_type = query_params.get("type", "overview") - contributions = self._get_author_contribution_queryset( - author.id, ordering, asset_type - ) - - page = self.paginate_queryset(contributions) - context = self._get_contribution_context(author.user_id) - serializer = DynamicContributionSerializer( - page, - _include_fields=[ - "contribution_type", - "created_date", - "id", - "source", - "created_by", - "unified_document", - "author", - ], - context=context, - many=True, - ) - data = serializer.data - response = self.get_paginated_response(data) - if asset_type == "bounty_offered": - total_bounty_amount = contributions.aggregate( - total_amount=Sum("bounty__amount") - ) - response.data["total_bounty_amount"] = total_bounty_amount.get( - "total_amount", 0 - ) - - return response - - def _get_author_comments(self, author_id): - author = self.get_object() - user = author.user - - if user: - user_threads = RhCommentModel.objects.filter(Q(created_by=user)) - return user_threads - return [] - - def _get_author_contribution_queryset(self, author_id, ordering, asset_type): - author_comments = self._get_author_comments(author_id) - rh_comment_content_type = ContentType.objects.get_for_model(RhCommentModel) - post_content_type = ContentType.objects.get_for_model(ResearchhubPost) - paper_content_type = ContentType.objects.get_for_model(Paper) - hypothesis_content_type = ContentType.objects.get_for_model(Hypothesis) - review_content_type = ContentType.objects.get_for_model(Review) - bounty_content_type = ContentType.objects.get_for_model(Bounty) - bounty_solution_content_type = ContentType.objects.get_for_model(BountySolution) - - types = asset_type.split(",") - - query = Q() - for asset_type in types: - if asset_type == "overview": - query |= Q( - Q( - unified_document__is_removed=False, - content_type=rh_comment_content_type, - # we filter by object_id instead of author_profile because - # sometimes there's contributions without a matching comment. - # this method ensures the comments exists. - object_id__in=author_comments, - contribution_type__in=[ - Contribution.COMMENTER, - ], - ) - | Q( - unified_document__is_removed=False, - user__author_profile=author_id, - content_type_id__in=[ - hypothesis_content_type, - paper_content_type, - post_content_type, - review_content_type, - ], - contribution_type__in=[ - Contribution.SUBMITTER, - Contribution.SUPPORTER, - ], - ) - ) - elif asset_type == "discussion": - query |= Q( - unified_document__is_removed=False, - user__author_profile=author_id, - content_type_id=post_content_type, - contribution_type__in=[Contribution.SUBMITTER], - ) - elif asset_type == "hypothesis": - query |= Q( - unified_document__is_removed=False, - user__author_profile=author_id, - content_type_id=hypothesis_content_type, - contribution_type__in=[Contribution.SUBMITTER], - ) - elif asset_type == "comment": - query |= Q( - unified_document__is_removed=False, - content_type=rh_comment_content_type, - # we filter by object_id instead of author_profile because - # sometimes there's contributions without a matching comment. - # this method ensures the comments exists. - object_id__in=author_comments, - contribution_type__in=[Contribution.COMMENTER], - ) - elif asset_type == "paper": - query |= Q( - unified_document__is_removed=False, - user__author_profile=author_id, - content_type_id=paper_content_type, - contribution_type__in=[Contribution.SUBMITTER], - ) - elif asset_type == "bounty_offered": - query |= Q( - unified_document__is_removed=False, - user__author_profile=author_id, - content_type_id=bounty_content_type, - contribution_type__in=[Contribution.BOUNTY_CREATED], - ) - elif asset_type == "bounty_earned": - query |= Q( - unified_document__is_removed=False, - user__author_profile=author_id, - content_type_id=bounty_solution_content_type, - contribution_type__in=[Contribution.BOUNTY_SOLUTION], - ) - else: - raise Exception("Unrecognized asset type: {}".format(asset_type)) - - qs = ( - Contribution.objects.filter(query) - .select_related( - "content_type", - "user", - "user__author_profile", - "unified_document", - ) - .order_by(ordering) - ) - - return qs - - @action( - detail=True, - methods=["get"], - ) - def get_user_discussions(self, request, pk=None): - author = self.get_object() - user = author.user - - if user: - user_discussions = user.thread_set.filter(is_removed=False).order_by("-id") - else: - user_discussions = self.queryset.none() - - page = self.paginate_queryset(user_discussions) - context = self._get_user_discussion_context() - serializer = DynamicThreadSerializer( - page, - _include_fields=[ - "id", - "comment_count", - "created_by", - "created_date", - "paper", - "post", - "score", - "text", - ], - many=True, - context=context, - ) - return self.get_paginated_response(serializer.data) - - def _get_user_discussion_context(self): - context = { - "dis_dts_get_created_by": { - "_include_fields": [ - "id", - "author_profile", - ] - }, - "dis_dts_get_paper": { - "_include_fields": [ - "id", - "slug", - ] - }, - "dis_dts_get_post": { - "_include_fields": [ - "id", - "slug", - ] - }, - "usr_dus_get_author_profile": { - "_include_fields": ["id", "first_name", "last_name", "profile_image"] - }, - } - return context - - @action( - detail=True, - methods=["get"], - ) - def get_user_contributions(self, request, pk=None): - author = self.get_object() - user = author.user - - if user: - prefetch_lookups = PaperViewSet.prefetch_lookups(self) - user_paper_uploads = user.papers.filter(is_removed=False).prefetch_related( - *prefetch_lookups - ) - else: - user_paper_uploads = self.queryset.none() - - context = self._get_user_contributions_context() - page = self.paginate_queryset(user_paper_uploads) - serializer = DynamicPaperSerializer( - page, - _include_fields=[ - "id", - "abstract", - "boost_amount", - "file", - "hubs", - "paper_title", - "score", - "title", - "slug", - "uploaded_by", - "uploaded_date", - ], - many=True, - context=context, - ) - response = self.get_paginated_response(serializer.data) - - return response - - def _get_user_contributions_context(self): - context = { - "pap_dps_get_uploaded_by": { - "_include_fields": [ - "id", - "author_profile", - ] - }, - "usr_dus_get_author_profile": { - "_include_fields": ["id", "first_name", "last_name", "profile_image"] - }, - "doc_duds_get_hubs": { - "_include_fields": [ - "id", - "name", - "slug", - "hub_image", - ] - }, - } - return context - - @action( - detail=True, - methods=["get"], - ) - def get_user_posts(self, request, pk=None): - author = self.get_object() - user = author.user - - if user: - user_posts = user.created_posts.all().prefetch_related( - "unified_document", "purchases" - ) - else: - user_posts = self.queryset.none() - - context = self._get_user_posts_context() - page = self.paginate_queryset(user_posts) - serializer = DynamicPostSerializer( - page, - _include_fields=[ - "id", - "created_by", - "hubs", - "boost_amount", - "renderable_text", - "score", - "slug", - "title", - ], - many=True, - context=context, - ) - response = self.get_paginated_response(serializer.data) - return response - - def _get_user_posts_context(self): - context = { - "doc_dps_get_created_by": { - "_include_fields": [ - "id", - "author_profile", - ] - }, - "usr_dus_get_author_profile": { - "_include_fields": ["id", "first_name", "last_name", "profile_image"] - }, - "doc_dps_get_hubs": { - "_include_fields": [ - "id", - "name", - "slug", - "hub_image", - ] - }, - } - return context diff --git a/src/utils/openalex.py b/src/utils/openalex.py index 492270696..f74bbe399 100644 --- a/src/utils/openalex.py +++ b/src/utils/openalex.py @@ -310,19 +310,50 @@ def get_topics(self, next_cursor="*", page=1, batch_size=100): cursor = next_cursor if next_cursor != "*" else None return topics, cursor + def get_authors( + self, + next_cursor="*", + batch_size=100, + openalex_ids=None, + ): + # Build the filter + oa_filters = [] + + if isinstance(openalex_ids, list): + oa_filters.append(f"ids.openalex:{'|'.join(openalex_ids)}") + + filters = { + "filter": ",".join(oa_filters), + "per-page": batch_size, + "cursor": next_cursor, + } + + response = self._get("authors", filters=filters) + authors = response.get("results", []) + next_cursor = response.get("meta", {}).get("next_cursor") + cursor = next_cursor if next_cursor != "*" else None + return authors, cursor + + def get_work( + self, + openalex_id=None, + ): + return self._get(f"works/{openalex_id}") + def get_works( self, since_date=None, - type=None, + types=None, next_cursor="*", batch_size=100, openalex_ids=None, source_id=None, + openalex_author_id=None, ): # Build the filter oa_filters = [] - if type: - oa_filters.append(f"type:{type}") + if isinstance(types, list): + oa_filters.append(f"type:{'|'.join(types)}") if source_id: oa_filters.append(f"primary_location.source.id:{source_id}") @@ -332,9 +363,12 @@ def get_works( formatted_date = since_date.strftime("%Y-%m-%d") oa_filters.append(f"from_created_date:{formatted_date}") - if openalex_ids: + if isinstance(openalex_ids, list): oa_filters.append(f"ids.openalex:{'|'.join(openalex_ids)}") + if openalex_author_id: + oa_filters.append(f"author.id:{openalex_author_id}") + filters = { "filter": ",".join(oa_filters), "per-page": batch_size,