├── .github ├── ISSUE_TEMPLATE.md └── workflows │ ├── deploy-web-app.yml │ └── test-server.yml ├── .gitignore ├── .gitmodules ├── LICENSE.md ├── README.md ├── auto-updater ├── bin_stats_updater.py ├── deployment │ ├── cron_jobs.txt │ └── setup.bash ├── downloader.py ├── get_square_bins.R ├── journal_centroid.py ├── json_minimizer.py ├── kd_tree_creator.py ├── main.py ├── merger.py ├── paper_parser.py ├── pkg-upgrade.bash ├── requirements.txt ├── run.bash ├── saucie_coordinates.py └── utils.py ├── frontend ├── .env ├── .eslintrc.yaml ├── .gitignore ├── README.md ├── package.json ├── public │ ├── data │ │ ├── filter-plot.html │ │ └── plot.json │ ├── icons │ │ ├── android-chrome-192x192.png │ │ ├── android-chrome-512x512.png │ │ ├── apple-touch-icon.png │ │ ├── browserconfig.xml │ │ ├── favicon-512x512.png │ │ ├── mstile-144x144.png │ │ ├── mstile-150x150.png │ │ ├── mstile-310x150.png │ │ ├── mstile-310x310.png │ │ ├── mstile-70x70.png │ │ ├── safari-pinned-tab.svg │ │ ├── share-thumbnail.png │ │ └── site.webmanifest │ └── index.html ├── src │ ├── about.js │ ├── app.css │ ├── app.js │ ├── backend.js │ ├── card.css │ ├── cell-details.css │ ├── cell-details.js │ ├── checkmark.svg │ ├── cloud-buttons.css │ ├── cloud-buttons.js │ ├── error.js │ ├── footer.js │ ├── header.css │ ├── header.js │ ├── hooks.js │ ├── index.js │ ├── legend.css │ ├── legend.js │ ├── logo.svg │ ├── map-sections.js │ ├── map.css │ ├── map.js │ ├── math.js │ ├── preprint-info.js │ ├── search.css │ ├── search.js │ ├── similar-journals.js │ ├── similar-papers.js │ ├── status.css │ └── status.js └── yarn.lock └── server ├── app_runner.py ├── deployment ├── cron_jobs.txt ├── launch-updater-vm.bash ├── nginx.conf ├── setup.bash ├── supervisor.conf └── update-data.bash ├── document_downloader.py ├── find_coordinates.py ├── find_knn.py ├── requirements.txt ├── saucie_model ├── SAUCIE.data-00000-of-00001 ├── SAUCIE.index ├── SAUCIE.meta └── checkpoint ├── settings.py ├── tests.py ├── utils.py └── word_vectors.py /.github/ISSUE_TEMPLATE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/.github/ISSUE_TEMPLATE.md -------------------------------------------------------------------------------- /.github/workflows/deploy-web-app.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/.github/workflows/deploy-web-app.yml -------------------------------------------------------------------------------- /.github/workflows/test-server.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/.github/workflows/test-server.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/.gitmodules -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/README.md -------------------------------------------------------------------------------- /auto-updater/bin_stats_updater.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/bin_stats_updater.py -------------------------------------------------------------------------------- /auto-updater/deployment/cron_jobs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/deployment/cron_jobs.txt -------------------------------------------------------------------------------- /auto-updater/deployment/setup.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/deployment/setup.bash -------------------------------------------------------------------------------- /auto-updater/downloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/downloader.py -------------------------------------------------------------------------------- /auto-updater/get_square_bins.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/get_square_bins.R -------------------------------------------------------------------------------- /auto-updater/journal_centroid.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/journal_centroid.py -------------------------------------------------------------------------------- /auto-updater/json_minimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/json_minimizer.py -------------------------------------------------------------------------------- /auto-updater/kd_tree_creator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/kd_tree_creator.py -------------------------------------------------------------------------------- /auto-updater/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/main.py -------------------------------------------------------------------------------- /auto-updater/merger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/merger.py -------------------------------------------------------------------------------- /auto-updater/paper_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/paper_parser.py -------------------------------------------------------------------------------- /auto-updater/pkg-upgrade.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/pkg-upgrade.bash -------------------------------------------------------------------------------- /auto-updater/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/requirements.txt -------------------------------------------------------------------------------- /auto-updater/run.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/run.bash -------------------------------------------------------------------------------- /auto-updater/saucie_coordinates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/saucie_coordinates.py -------------------------------------------------------------------------------- /auto-updater/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/auto-updater/utils.py -------------------------------------------------------------------------------- /frontend/.env: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/.env -------------------------------------------------------------------------------- /frontend/.eslintrc.yaml: -------------------------------------------------------------------------------- 1 | extends: 2 | - react-app 3 | -------------------------------------------------------------------------------- /frontend/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/.gitignore -------------------------------------------------------------------------------- /frontend/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/README.md -------------------------------------------------------------------------------- /frontend/package.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/package.json -------------------------------------------------------------------------------- /frontend/public/data/filter-plot.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/data/filter-plot.html -------------------------------------------------------------------------------- /frontend/public/data/plot.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/data/plot.json -------------------------------------------------------------------------------- /frontend/public/icons/android-chrome-192x192.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/android-chrome-192x192.png -------------------------------------------------------------------------------- /frontend/public/icons/android-chrome-512x512.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/android-chrome-512x512.png -------------------------------------------------------------------------------- /frontend/public/icons/apple-touch-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/apple-touch-icon.png -------------------------------------------------------------------------------- /frontend/public/icons/browserconfig.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/browserconfig.xml -------------------------------------------------------------------------------- /frontend/public/icons/favicon-512x512.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/favicon-512x512.png -------------------------------------------------------------------------------- /frontend/public/icons/mstile-144x144.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/mstile-144x144.png -------------------------------------------------------------------------------- /frontend/public/icons/mstile-150x150.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/mstile-150x150.png -------------------------------------------------------------------------------- /frontend/public/icons/mstile-310x150.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/mstile-310x150.png -------------------------------------------------------------------------------- /frontend/public/icons/mstile-310x310.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/mstile-310x310.png -------------------------------------------------------------------------------- /frontend/public/icons/mstile-70x70.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/mstile-70x70.png -------------------------------------------------------------------------------- /frontend/public/icons/safari-pinned-tab.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/safari-pinned-tab.svg -------------------------------------------------------------------------------- /frontend/public/icons/share-thumbnail.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/share-thumbnail.png -------------------------------------------------------------------------------- /frontend/public/icons/site.webmanifest: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/icons/site.webmanifest -------------------------------------------------------------------------------- /frontend/public/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/public/index.html -------------------------------------------------------------------------------- /frontend/src/about.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/about.js -------------------------------------------------------------------------------- /frontend/src/app.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/app.css -------------------------------------------------------------------------------- /frontend/src/app.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/app.js -------------------------------------------------------------------------------- /frontend/src/backend.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/backend.js -------------------------------------------------------------------------------- /frontend/src/card.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/card.css -------------------------------------------------------------------------------- /frontend/src/cell-details.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/cell-details.css -------------------------------------------------------------------------------- /frontend/src/cell-details.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/cell-details.js -------------------------------------------------------------------------------- /frontend/src/checkmark.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/checkmark.svg -------------------------------------------------------------------------------- /frontend/src/cloud-buttons.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/cloud-buttons.css -------------------------------------------------------------------------------- /frontend/src/cloud-buttons.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/cloud-buttons.js -------------------------------------------------------------------------------- /frontend/src/error.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/error.js -------------------------------------------------------------------------------- /frontend/src/footer.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/footer.js -------------------------------------------------------------------------------- /frontend/src/header.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/header.css -------------------------------------------------------------------------------- /frontend/src/header.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/header.js -------------------------------------------------------------------------------- /frontend/src/hooks.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/hooks.js -------------------------------------------------------------------------------- /frontend/src/index.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/index.js -------------------------------------------------------------------------------- /frontend/src/legend.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/legend.css -------------------------------------------------------------------------------- /frontend/src/legend.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/legend.js -------------------------------------------------------------------------------- /frontend/src/logo.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/logo.svg -------------------------------------------------------------------------------- /frontend/src/map-sections.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/map-sections.js -------------------------------------------------------------------------------- /frontend/src/map.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/map.css -------------------------------------------------------------------------------- /frontend/src/map.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/map.js -------------------------------------------------------------------------------- /frontend/src/math.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/math.js -------------------------------------------------------------------------------- /frontend/src/preprint-info.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/preprint-info.js -------------------------------------------------------------------------------- /frontend/src/search.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/search.css -------------------------------------------------------------------------------- /frontend/src/search.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/search.js -------------------------------------------------------------------------------- /frontend/src/similar-journals.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/similar-journals.js -------------------------------------------------------------------------------- /frontend/src/similar-papers.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/similar-papers.js -------------------------------------------------------------------------------- /frontend/src/status.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/status.css -------------------------------------------------------------------------------- /frontend/src/status.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/src/status.js -------------------------------------------------------------------------------- /frontend/yarn.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/frontend/yarn.lock -------------------------------------------------------------------------------- /server/app_runner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/app_runner.py -------------------------------------------------------------------------------- /server/deployment/cron_jobs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/deployment/cron_jobs.txt -------------------------------------------------------------------------------- /server/deployment/launch-updater-vm.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/deployment/launch-updater-vm.bash -------------------------------------------------------------------------------- /server/deployment/nginx.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/deployment/nginx.conf -------------------------------------------------------------------------------- /server/deployment/setup.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/deployment/setup.bash -------------------------------------------------------------------------------- /server/deployment/supervisor.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/deployment/supervisor.conf -------------------------------------------------------------------------------- /server/deployment/update-data.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/deployment/update-data.bash -------------------------------------------------------------------------------- /server/document_downloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/document_downloader.py -------------------------------------------------------------------------------- /server/find_coordinates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/find_coordinates.py -------------------------------------------------------------------------------- /server/find_knn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/find_knn.py -------------------------------------------------------------------------------- /server/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/requirements.txt -------------------------------------------------------------------------------- /server/saucie_model/SAUCIE.data-00000-of-00001: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/saucie_model/SAUCIE.data-00000-of-00001 -------------------------------------------------------------------------------- /server/saucie_model/SAUCIE.index: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/saucie_model/SAUCIE.index -------------------------------------------------------------------------------- /server/saucie_model/SAUCIE.meta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/saucie_model/SAUCIE.meta -------------------------------------------------------------------------------- /server/saucie_model/checkpoint: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/saucie_model/checkpoint -------------------------------------------------------------------------------- /server/settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/settings.py -------------------------------------------------------------------------------- /server/tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/tests.py -------------------------------------------------------------------------------- /server/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/utils.py -------------------------------------------------------------------------------- /server/word_vectors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/preprint-similarity-search/HEAD/server/word_vectors.py --------------------------------------------------------------------------------