├── .github ├── CODEOWNERS ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ └── on_push.yaml ├── .gitignore ├── LICENSE ├── README.md ├── data ├── external │ └── .gitkeep └── processed │ └── .gitkeep ├── pyproject.toml ├── scripts ├── add_docs.py ├── data │ ├── README.md │ ├── concept_rate.py │ ├── filter_AMiner.py │ └── get_AMiner.py ├── requirements.txt └── wikipedia │ ├── convert_taxonomy.py │ └── create_taxonomy.py ├── setup.sh ├── src ├── __init__.py ├── backend │ ├── __init__.py │ ├── ml_api │ │ ├── README.md │ │ ├── __init__.py │ │ ├── app.py │ │ ├── classifiers │ │ │ ├── binary │ │ │ │ ├── __init__.py │ │ │ │ ├── base.py │ │ │ │ ├── dummy.py │ │ │ │ └── fasttext_classifier.py │ │ │ └── prompt │ │ │ │ ├── __init__.py │ │ │ │ └── gpt_classifier.py │ │ ├── conftest.py │ │ ├── external_models │ │ │ ├── __init__.py │ │ │ └── transformers_model.py │ │ ├── routers │ │ │ ├── __init__.py │ │ │ ├── classify.py │ │ │ ├── model.py │ │ │ ├── question.py │ │ │ └── summarize.py │ │ ├── tests │ │ │ └── test_classifiers.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── device.py │ │ │ └── logging_config.py │ └── search_app │ │ ├── README.md │ │ ├── docker-compose-juno.yml │ │ ├── docker-compose.yml │ │ ├── requirements.txt │ │ ├── search_app.Dockerfile │ │ ├── search_app.py │ │ ├── search_app_config.json │ │ └── templates │ │ └── index.html └── cruise_literature │ ├── citation_screening │ ├── README.md │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_alter_literaturereview_first_screening.py │ │ ├── 0003_literaturereview_exclusion_criteria_and_more.py │ │ ├── 0004_remove_literaturereview_exclusion_criteria_and_more.py │ │ ├── 0005_literaturereview_exclusion_criteria_and_more.py │ │ ├── 0006_remove_literaturereviewmember_user_and_more.py │ │ ├── 0007_remove_literaturereview_first_screening_and_more.py │ │ ├── 0008_alter_literaturereview_tags.py │ │ ├── 0009_literaturereview_created_at_and_more.py │ │ ├── 0010_literaturereview_organisation.py │ │ ├── 0011_remove_literaturereview_creation_date_and_more.py │ │ ├── 0012_alter_literaturereview_data_format_version.py │ │ ├── 0013_remove_literaturereview_discipline_and_more.py │ │ ├── 0014_alter_citationscreening_literature_review_and_more.py │ │ ├── 0015_citationscreening_tasks_updated_at.py │ │ ├── 0016_citationscreening_distributed_papers.py │ │ └── __init__.py │ ├── models.py │ ├── tests.py │ ├── urls.py │ └── views.py │ ├── cruise_literature │ ├── __init__.py │ ├── asgi.py │ ├── settings.py │ ├── urls.py │ └── wsgi.py │ ├── cruise_rag │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_remove_llmconversation_id_and_more.py │ │ └── __init__.py │ ├── models.py │ ├── tests.py │ ├── urls.py │ └── views.py │ ├── docker-compose.yaml │ ├── document_classification │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── classifiers │ │ ├── __init__.py │ │ ├── base.py │ │ ├── dummy.py │ │ ├── fasttext_classifier.py │ │ └── tests.py │ ├── migrations │ │ ├── 0001_initial.py │ │ └── __init__.py │ ├── models.py │ ├── registry.py │ ├── serializers.py │ ├── tests.py │ ├── urls.py │ └── views.py │ ├── document_search │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── engine_logger.py │ ├── fixtures │ │ └── search_engines.json │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_remove_searchengine_is_available_and_more.py │ │ └── __init__.py │ ├── models.py │ ├── search_core.py │ ├── search_cruise.py │ ├── search_google_scholar.py │ ├── search_pubmed.py │ ├── search_semantic_scholar.py │ ├── search_wikipedia.py │ ├── tests.py │ ├── urls.py │ ├── utils.py │ └── views.py │ ├── home │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── migrations │ │ └── __init__.py │ ├── models.py │ ├── tests.py │ ├── urls.py │ └── views.py │ ├── literature_review │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── forms.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_literaturereviewmember_added_by.py │ │ ├── 0003_literaturereview_papers_updated_at_and_more.py │ │ ├── 0004_remove_literaturereview_min_decisions.py │ │ ├── 0005_alter_literaturereview_ready_for_screening.py │ │ ├── 0006_remove_literaturereview_exclusion_criteria_and_more.py │ │ ├── 0007_literaturereview_review_type.py │ │ └── __init__.py │ ├── models.py │ ├── tests.py │ ├── urls.py │ └── views.py │ ├── manage.py │ ├── organisations │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── forms.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_alter_organisation_created_by.py │ │ ├── 0003_rename_user_organisationmember_member.py │ │ └── __init__.py │ ├── models.py │ ├── tests.py │ ├── urls.py │ └── views.py │ ├── static │ ├── css │ │ ├── bulma-calendar.min.css │ │ └── style.css │ ├── favicon │ │ └── favicon.ico │ ├── img │ │ ├── cruise-logo-small.png │ │ ├── cruise-logo.png │ │ ├── pdf-icon.svg │ │ └── wikipedia-logo.png │ └── js │ │ ├── bulma-calendar.min.js │ │ ├── modal.js │ │ └── sort-paginate-table.js │ ├── templates │ ├── _base_templates │ │ ├── _base.html │ │ ├── _footer.html │ │ └── _header.html │ ├── document_search │ │ ├── _card.html │ │ ├── _search_result_list.html │ │ ├── _search_small.html │ │ ├── _wikipedia_card.html │ │ └── plain_search.html │ ├── home │ │ ├── about.html │ │ ├── faq.html │ │ └── home.html │ ├── literature_review │ │ ├── _review_header.html │ │ ├── add_review_member.html │ │ ├── add_seed_studies.html │ │ ├── create_literature_review.html │ │ ├── edit_literature_review.html │ │ ├── home.html │ │ ├── import_papers.html │ │ ├── manage_review.html │ │ ├── remove_review_member.html │ │ ├── screen_paper.html │ │ ├── screening_home.html │ │ └── view_review.html │ ├── organisations │ │ ├── add_member.html │ │ ├── create_organisation.html │ │ ├── view_all_organisations.html │ │ └── view_organisation.html │ └── users │ │ ├── edit_user_profile.html │ │ ├── login.html │ │ ├── register.html │ │ └── user_profile.html │ ├── users │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── fixtures │ │ └── users_data.json │ ├── forms.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_user_allow_logging_user_preferred_taxonomies.py │ │ └── __init__.py │ ├── models.py │ ├── tests.py │ ├── urls.py │ └── views.py │ └── utils │ ├── article.py │ ├── django_tags.py │ └── process_pdf.py └── uv.lock /.github/CODEOWNERS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ProjectDossier/cruise-screening/HEAD/.github/CODEOWNERS -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ProjectDossier/cruise-screening/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- 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