From c488e5fdce07729d31b971e116e7de21511c5f42 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 20 Aug 2024 09:11:14 -0400 Subject: [PATCH 01/17] add temporary explore page text --- src/App.jsx | 4 ++++ src/components/header/Header.jsx | 1 + src/pages/Explore.jsx | 17 +++++++++++++++++ 3 files changed, 22 insertions(+) create mode 100644 src/pages/Explore.jsx diff --git a/src/App.jsx b/src/App.jsx index 72f2bda2..a32c1f9f 100644 --- a/src/App.jsx +++ b/src/App.jsx @@ -11,6 +11,7 @@ import Guide from '~/pages/Guide'; import Tutorial from '~/pages/Tutorial'; import TermsofService from '~/pages/TermsofService'; import QueryBuilder from '~/pages/queryBuilder/QueryBuilder'; +import Explore from '~/pages/Explore'; import Answer from '~/pages/answer/Answer'; import QuestionList from '~/pages/questionList/QuestionList'; @@ -72,6 +73,9 @@ export default function App() { + + + diff --git a/src/components/header/Header.jsx b/src/components/header/Header.jsx index de5152b8..58097a17 100644 --- a/src/components/header/Header.jsx +++ b/src/components/header/Header.jsx @@ -14,6 +14,7 @@ export default function Header() {
Question Builder + Explore About Guide Tutorial diff --git a/src/pages/Explore.jsx b/src/pages/Explore.jsx new file mode 100644 index 00000000..b7e01b5a --- /dev/null +++ b/src/pages/Explore.jsx @@ -0,0 +1,17 @@ +import React from 'react'; + +import { + Grid, Row, Col, +} from 'react-bootstrap'; + +export default function Explore() { + return ( + + + + Lorem, ipsum dolor sit amet consectetur adipisicing elit. Quo illum rem quam alias. Nam, ipsum velit. Necessitatibus aspernatur excepturi magnam cumque blanditiis illo optio? Perferendis inventore corporis neque deleniti? In veniam dolore ipsum, eveniet sit blanditiis, exercitationem expedita facilis mollitia neque similique, ducimus nemo saepe sapiente vitae at repellendus modi sequi excepturi! Fuga nisi est quia. Nesciunt optio enim, facere similique pariatur assumenda alias sint laudantium velit! Eum, praesentium ducimus ipsum dignissimos beatae nostrum maiores molestiae assumenda modi repellat alias obcaecati esse ab totam sunt iure, itaque quis ratione, veritatis sapiente vel repellendus libero illo. Dolores neque, animi, libero a accusamus consequatur doloribus nam mollitia obcaecati quos aliquid ex et qui nemo modi non dolorem? Minima fuga pariatur fugit eaque amet autem voluptatibus quae voluptates repellat, dolorem sequi quidem accusamus suscipit ut necessitatibus quaerat esse dolor quisquam ullam deleniti in veritatis, quod enim odio? Illum dolorem unde, quis soluta, eligendi, atque voluptatem omnis molestias minima error eius praesentium incidunt? Assumenda commodi voluptatibus eos eius cupiditate sunt consectetur libero. Incidunt deleniti excepturi temporibus consectetur deserunt quas repellat, perspiciatis voluptatibus ad odit earum provident beatae! Officia delectus, deserunt aliquid placeat rerum in facilis perferendis optio magnam molestias nisi autem atque voluptatem quibusdam velit quod dolore vitae enim. Mollitia eum laboriosam itaque repellendus nesciunt, ducimus quidem veritatis laborum laudantium, pariatur cupiditate numquam quasi. Sequi iusto soluta sed adipisci illo similique repudiandae consequatur optio non commodi recusandae eius sapiente aliquam saepe nam iure cumque ipsum, perferendis modi quaerat cupiditate qui obcaecati vel? Modi quisquam quae sed ut eveniet consequatur quos doloremque? Quisquam fugit sapiente, dignissimos, ad fuga ipsa accusantium delectus at quod enim, quis alias doloribus odio tempora! Perferendis, dolore assumenda soluta earum eligendi quisquam necessitatibus repellendus perspiciatis tenetur accusantium laborum. Explicabo libero voluptas eaque omnis saepe dignissimos nesciunt, odit dolores fugiat magnam, officiis aspernatur? Numquam eos amet eligendi aut quia necessitatibus quasi architecto laborum in dicta earum fugiat ad nulla sint nemo placeat voluptate eius id error blanditiis, ex aperiam quibusdam nobis. In non, culpa ipsa nemo minima earum fuga. Perspiciatis minima pariatur quo, illum voluptate velit eos suscipit tempore eligendi aliquid provident facilis in, omnis fugit tenetur voluptatum adipisci asperiores ipsam nihil! Voluptatem et omnis quos modi officiis eveniet debitis commodi quia, deserunt rerum corporis, at cumque expedita dolorem voluptates assumenda! Doloribus officiis dicta impedit architecto, eaque quasi sit non quae voluptatem, possimus omnis expedita et a consectetur fugiat facere distinctio facilis aspernatur itaque beatae mollitia deserunt assumenda, vitae provident! Exercitationem similique, unde rem cumque expedita assumenda eum nostrum, voluptatibus adipisci quod recusandae debitis rerum praesentium animi, possimus eaque ab tenetur sequi necessitatibus! Ex dolor necessitatibus dolorum tenetur dicta quos natus vitae repellat cupiditate alias. Ad consequuntur nobis exercitationem laborum aperiam, voluptas culpa eos, iure velit minima harum hic magni. Nisi eveniet molestiae quis tenetur placeat. Rem, obcaecati? Corrupti atque vitae eaque tempore et animi? Sit molestiae cupiditate omnis ea earum maiores fuga, cum obcaecati inventore laborum quia tenetur saepe accusantium neque? Placeat, consectetur eum dignissimos aliquam neque quibusdam doloribus cupiditate blanditiis? + + + + ); +} From 6d3187bf551726ede50dd550d5f2f4081faeebd7 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 20 Aug 2024 10:50:59 -0400 Subject: [PATCH 02/17] add explore page --- api_routes/drug-disease.json | 5002 ++++++++++++++++++++++++++++++++++ api_routes/routes.js | 6 + src/pages/Explore.jsx | 161 +- 3 files changed, 5161 insertions(+), 8 deletions(-) create mode 100644 api_routes/drug-disease.json diff --git a/api_routes/drug-disease.json b/api_routes/drug-disease.json new file mode 100644 index 00000000..79576fb5 --- /dev/null +++ b/api_routes/drug-disease.json @@ -0,0 +1,5002 @@ +[ + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0018616", + "name": "central serous chorioretinopathy" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0021667", + "name": "neuralgia" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "UMLS:C3854347", + "name": "Intentional product misuse" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "UMLS:C3805175", + "name": "Appendicolith" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0002203", + "name": "constipation disorder" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0043726", + "name": "multiple organ dysfunction syndrome" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0009688", + "name": "myasthenia gravis" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005113", + "name": "bacterial infectious disease" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0800175", + "name": "cardiogenic shock" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0000190", + "name": "ventricular fibrillation" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0017291", + "name": "reversible cerebral vasoconstriction syndrome" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005649", + "name": "appendicitis" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005298", + "name": "osteoporosis" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005420", + "name": "hypothyroidism" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005083", + "name": "psoriasis" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0003014", + "name": "rhinitis" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005441", + "name": "otitis media" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005709", + "name": "common cold" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005961", + "name": "sinusitis" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005108", + "name": "viral infectious disease" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0000740", + "name": "adenoid hypertrophy" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0004425", + "name": "hyperthyroidism" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005044", + "name": "hypertensive disorder" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005015", + "name": "diabetes mellitus" + } + }, + { + "drug": { + "id": "CHEBI:10082", + "name": "xylometazoline" + }, + "disease": { + "id": "MONDO:0005267", + "name": "heart disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0001358", + "name": "bronchial disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005146", + "name": "post-traumatic stress disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0006731", + "name": "drug-induced akathisia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "UMLS:C0001969", + "name": "Alcoholic Intoxication" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005383", + "name": "panic disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002025", + "name": "psychiatric disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005618", + "name": "anxiety disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0004681", + "name": "learning disability" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002494", + "name": "substance-related disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0007743", + "name": "attention deficit-hyperactivity disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0004456", + "name": "cocaine abuse" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005530", + "name": "opiate dependence" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002134", + "name": "physiological sexual disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0001106", + "name": "kidney failure" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0004985", + "name": "bipolar disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005567", + "name": "substance withdrawal syndrome" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005804", + "name": "hyperprolactinemia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0100192", + "name": "liver failure" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0007774", + "name": "hyperreflexia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0001286", + "name": "exotropia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "UMLS:C0011609", + "name": "Drug Eruptions" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005302", + "name": "attention deficit hyperactivity disorder, inattentive type" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0004985", + "name": "bipolar disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0022578", + "name": "childhood bladder carcinoma" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005105", + "name": "melanoma" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0006732", + "name": "drug-induced dyskinesia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005178", + "name": "osteoarthritis" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002009", + "name": "major depressive disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002032", + "name": "colon carcinoma" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0021063", + "name": "malignant colon neoplasm" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002277", + "name": "arteriosclerosis disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0007803", + "name": "multiple system atrophy" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005311", + "name": "atherosclerosis" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0011122", + "name": "obesity disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005146", + "name": "post-traumatic stress disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "UMLS:C0027055", + "name": "Myocardial Reperfusion Injury" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002909", + "name": "hyperglycemia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0007263", + "name": "cardiac rhythm disease" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005010", + "name": "coronary artery disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005148", + "name": "type 2 diabetes mellitus" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005466", + "name": "hypersomnia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005383", + "name": "panic disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005300", + "name": "chronic kidney disease" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005015", + "name": "diabetes mellitus" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005395", + "name": "movement disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "UMLS:C0525041", + "name": "Neurobehavioral Manifestations" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005302", + "name": "attention deficit hyperactivity disorder, inattentive type" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002342", + "name": "chondromalacia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005468", + "name": "hypotensive disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0004992", + "name": "cancer" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005091", + "name": "severe acute respiratory syndrome" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005047", + "name": "infertility disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0007743", + "name": "attention deficit-hyperactivity disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0007661", + "name": "Tourette syndrome" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0002909", + "name": "hyperglycemia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005192", + "name": "exocrine pancreatic carcinoma" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0005362", + "name": "erectile dysfunction" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0000837", + "name": "bone resorption disease" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0018608", + "name": "pure autonomic failure" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0001384", + "name": "myopia" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0007254", + "name": "breast cancer" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0000947", + "name": "psychosexual disorder" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": "yohimbine" + }, + "disease": { + "id": "MONDO:0009831", + "name": "malignant pancreatic neoplasm" + } + }, + { + "drug": { + "id": "CHEBI:10093", + "name": 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"polyneuropathy" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005344", + "name": "hepatitis B virus infection" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0018177", + "name": "glioblastoma" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005109", + "name": "HIV infectious disease" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005550", + "name": "infectious disease" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0021063", + "name": "malignant colon neoplasm" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0004790", + "name": "fatty liver disease" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0011996", + "name": "chronic myelogenous leukemia, BCR-ABL1 positive" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0012268", + "name": "AIDS" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005108", + "name": "viral infectious disease" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0021042", + "name": "glioma" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005192", + "name": "exocrine pancreatic carcinoma" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0017769", + "name": "acquired immunodeficiency" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0100430", + "name": "fibrotic liver disease" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0043479", + "name": "adenoviridae infectious disease" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005184", + "name": "pancreatic ductal adenocarcinoma" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0007254", + "name": "breast cancer" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005233", + "name": "non-small cell lung carcinoma" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0009831", + "name": "malignant pancreatic neoplasm" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0021094", + "name": "immunodeficiency disease" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0002321", + "name": "sensory peripheral neuropathy" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005155", + "name": "cirrhosis of liver" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0004992", + "name": "cancer" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0007256", + "name": "hepatocellular carcinoma" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005105", + "name": "melanoma" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0021040", + "name": "pancreatic neoplasm" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0002251", + "name": "hepatitis" + } + }, + { + "drug": { + "id": "CHEBI:10101", + "name": "zalcitabine" + }, + "disease": { + "id": "MONDO:0005109", + "name": "HIV infectious disease" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005395", + "name": "movement disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0011918", + "name": "anxiety" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0000437", + "name": "cerebellar ataxia" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0001165", + "name": "tongue disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005292", + "name": "colitis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "UMLS:C0919980", + "name": "VIIth nerve palsy" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0002471", + "name": "bursitis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005071", + "name": "nervous system disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0003159", + "name": "vascular hemostatic disease" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0002909", + "name": "hyperglycemia" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0006547", + "name": "exanthem" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0003799", + "name": "conjunctivitis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0004848", + "name": "ulcerative stomatitis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0002610", + "name": "purpura" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005469", + "name": "orthostatic hypotension" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0004980", + "name": "atopic eczema" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "UMLS:C0340865", + "name": "Anaphylactoid Reaction" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0002657", + "name": "breast disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005083", + "name": "psoriasis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0013600", + "name": "insomnia" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005351", + "name": "anorexia nervosa" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "UMLS:C0403632", + "name": "Non-Infectious Cystitis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0006771", + "name": "glossitis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0004247", + "name": "peptic ulcer disease" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "UMLS:C0233494", + "name": "Tension" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "UMLS:C2047937", + "name": "Ill-defined disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0019337", + "name": "autoimmune bullous skin disease" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005328", + "name": "eye disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0004565", + "name": "intestinal obstruction" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0100053", + "name": "anaphylaxis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0004730", + "name": "speech disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0002102", + "name": "cheilitis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "UMLS:C0233414", + "name": "Disturbance of attention" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0015691", + "name": "hypereosinophilic syndrome" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0000736", + "name": "dyschromatosis universalis hereditaria" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005279", + "name": "pulmonary embolism" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005137", + "name": "nutritional disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "UMLS:C0151547", + "name": "Cataract specified" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005178", + "name": "osteoarthritis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0005578", + "name": "arthritic joint disease" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0043303", + "name": "hyperacusis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0001152", + "name": "amnestic disorder" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0004843", + "name": "pathologic nystagmus" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "UMLS:C0340464", + "name": "Premature Cardiac Complex" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0023557", + "name": "infective vaginitis" + } + }, + { + "drug": { + "id": "CHEBI:10102", + "name": "zaleplon" + }, + "disease": { + "id": "MONDO:0008698", + "name": "achalasia" + } + } +] \ No newline at end of file diff --git a/api_routes/routes.js b/api_routes/routes.js index 4e8f55c3..53dd100e 100644 --- a/api_routes/routes.js +++ b/api_routes/routes.js @@ -10,6 +10,7 @@ const services = require('./services'); const external_apis = require('./external'); const samples = JSON.parse(fs.readFileSync(path.join(__dirname, './sample-query-cache.json'))); +const drugDiseasePairs = JSON.parse(fs.readFileSync(path.join(__dirname, './drug-disease.json'))); router.use('/', external_apis); @@ -58,6 +59,11 @@ router.route('/quick_answer') } }); +router.route('/explore') + .post(async (req, res) => { + res.status(200).send(drugDiseasePairs); + }); + router.route('/answer') .post(async (req, res) => { const { questionId, ara } = req.query; diff --git a/src/pages/Explore.jsx b/src/pages/Explore.jsx index b7e01b5a..56abb54e 100644 --- a/src/pages/Explore.jsx +++ b/src/pages/Explore.jsx @@ -1,17 +1,162 @@ +import { Button, makeStyles } from '@material-ui/core'; +import { ArrowRight } from '@material-ui/icons'; import React from 'react'; - import { Grid, Row, Col, } from 'react-bootstrap'; +import { useHistory } from 'react-router-dom'; +import QueryBuilderContext from '~/context/queryBuilder'; +import useQueryBuilder from './queryBuilder/useQueryBuilder'; + +const useStyles = makeStyles({ + hover: { + '& .MuiButtonBase-root': { + visibility: 'hidden', + }, + '&:hover .MuiButtonBase-root': { + visibility: 'visible', + }, + }, +}); + +const fetchPairs = async () => { + const res = await fetch('/api/explore', { method: 'POST' }); + if (!res.ok) throw new Error(res.statusText); + return res.json(); +}; export default function Explore() { + const [pairs, setPairs] = React.useState([]); + const [isLoading, setIsLoading] = React.useState(true); + + // eslint-disable-next-line no-unused-vars + const [error, setError] = React.useState(null); + + const queryBuilder = useQueryBuilder(QueryBuilderContext); + const history = useHistory(); + + const handleStartQuery = (pair) => { + const query = { + message: { + query_graph: { + nodes: { + n0: { + name: pair.disease.name, + ids: [pair.disease.id], + }, + n1: { + name: pair.drug.name, + ids: [pair.drug.id], + }, + }, + edges: { + e0: { + subject: 'n0', + object: 'n1', + predicates: [ + 'biolink:related_to', + ], + }, + }, + }, + }, + }; + + queryBuilder.dispatch({ type: 'saveGraph', payload: query }); + history.push('/'); + }; + + const classes = useStyles(); + + React.useEffect(() => { + let ignore = false; + + (async () => { + try { + const data = await fetchPairs(); + + if (ignore) return; + + setPairs(data); + setIsLoading(false); + } catch (e) { + setError(e.message); + setIsLoading(false); + } + })(); + + return () => { + ignore = true; + }; + }, []); + + return ( + + + + +

Drug - Disease Pairs

+

+ These drug-disease pairs were generated using a machine learning model to align with the nodes + in the ROBOKOP knowledge graph. They highlight potential associations between various drugs and + a broad range of diseases, suggesting possible avenues for further research. These connections + can serve as a starting point for a new query by hovering over a pair and clicking “Start a Query”. +

+ +
+ + {isLoading ? 'Loading...' : ( + + + + + + + + + { + pairs.map((pair, i) => ( + + + + + + )) + } + +
+

Disease

+ 		+

Drug

+
+ {pair.disease.name} + {pair.disease.id} + + {pair.drug.name} + {pair.drug.id} +
+ )} + + + + + ); +} + +function Chip({ children }) { return ( - - - - Lorem, ipsum dolor sit amet consectetur adipisicing elit. Quo illum rem quam alias. Nam, ipsum velit. Necessitatibus aspernatur excepturi magnam cumque blanditiis illo optio? Perferendis inventore corporis neque deleniti? In veniam dolore ipsum, eveniet sit blanditiis, exercitationem expedita facilis mollitia neque similique, ducimus nemo saepe sapiente vitae at repellendus modi sequi excepturi! Fuga nisi est quia. Nesciunt optio enim, facere similique pariatur assumenda alias sint laudantium velit! Eum, praesentium ducimus ipsum dignissimos beatae nostrum maiores molestiae assumenda modi repellat alias obcaecati esse ab totam sunt iure, itaque quis ratione, veritatis sapiente vel repellendus libero illo. Dolores neque, animi, libero a accusamus consequatur doloribus nam mollitia obcaecati quos aliquid ex et qui nemo modi non dolorem? Minima fuga pariatur fugit eaque amet autem voluptatibus quae voluptates repellat, dolorem sequi quidem accusamus suscipit ut necessitatibus quaerat esse dolor quisquam ullam deleniti in veritatis, quod enim odio? Illum dolorem unde, quis soluta, eligendi, atque voluptatem omnis molestias minima error eius praesentium incidunt? Assumenda commodi voluptatibus eos eius cupiditate sunt consectetur libero. Incidunt deleniti excepturi temporibus consectetur deserunt quas repellat, perspiciatis voluptatibus ad odit earum provident beatae! Officia delectus, deserunt aliquid placeat rerum in facilis perferendis optio magnam molestias nisi autem atque voluptatem quibusdam velit quod dolore vitae enim. Mollitia eum laboriosam itaque repellendus nesciunt, ducimus quidem veritatis laborum laudantium, pariatur cupiditate numquam quasi. Sequi iusto soluta sed adipisci illo similique repudiandae consequatur optio non commodi recusandae eius sapiente aliquam saepe nam iure cumque ipsum, perferendis modi quaerat cupiditate qui obcaecati vel? Modi quisquam quae sed ut eveniet consequatur quos doloremque? Quisquam fugit sapiente, dignissimos, ad fuga ipsa accusantium delectus at quod enim, quis alias doloribus odio tempora! Perferendis, dolore assumenda soluta earum eligendi quisquam necessitatibus repellendus perspiciatis tenetur accusantium laborum. Explicabo libero voluptas eaque omnis saepe dignissimos nesciunt, odit dolores fugiat magnam, officiis aspernatur? Numquam eos amet eligendi aut quia necessitatibus quasi architecto laborum in dicta earum fugiat ad nulla sint nemo placeat voluptate eius id error blanditiis, ex aperiam quibusdam nobis. In non, culpa ipsa nemo minima earum fuga. Perspiciatis minima pariatur quo, illum voluptate velit eos suscipit tempore eligendi aliquid provident facilis in, omnis fugit tenetur voluptatum adipisci asperiores ipsam nihil! Voluptatem et omnis quos modi officiis eveniet debitis commodi quia, deserunt rerum corporis, at cumque expedita dolorem voluptates assumenda! Doloribus officiis dicta impedit architecto, eaque quasi sit non quae voluptatem, possimus omnis expedita et a consectetur fugiat facere distinctio facilis aspernatur itaque beatae mollitia deserunt assumenda, vitae provident! Exercitationem similique, unde rem cumque expedita assumenda eum nostrum, voluptatibus adipisci quod recusandae debitis rerum praesentium animi, possimus eaque ab tenetur sequi necessitatibus! Ex dolor necessitatibus dolorum tenetur dicta quos natus vitae repellat cupiditate alias. Ad consequuntur nobis exercitationem laborum aperiam, voluptas culpa eos, iure velit minima harum hic magni. Nisi eveniet molestiae quis tenetur placeat. Rem, obcaecati? Corrupti atque vitae eaque tempore et animi? Sit molestiae cupiditate omnis ea earum maiores fuga, cum obcaecati inventore laborum quia tenetur saepe accusantium neque? Placeat, consectetur eum dignissimos aliquam neque quibusdam doloribus cupiditate blanditiis? - - - + + {children} + ); } From 649baa315d62d8550acfb02e818cccecf428f935 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 20 Aug 2024 10:52:21 -0400 Subject: [PATCH 03/17] remove extra query builder context provider --- src/pages/Explore.jsx | 110 +++++++++++++++++++++--------------------- 1 file changed, 54 insertions(+), 56 deletions(-) diff --git a/src/pages/Explore.jsx b/src/pages/Explore.jsx index 56abb54e..10def6eb 100644 --- a/src/pages/Explore.jsx +++ b/src/pages/Explore.jsx @@ -91,62 +91,60 @@ export default function Explore() { }, []); return ( - - - - -

Drug - Disease Pairs

-

- These drug-disease pairs were generated using a machine learning model to align with the nodes - in the ROBOKOP knowledge graph. They highlight potential associations between various drugs and - a broad range of diseases, suggesting possible avenues for further research. These connections - can serve as a starting point for a new query by hovering over a pair and clicking “Start a Query”. -

- -
- - {isLoading ? 'Loading...' : ( - - - - - - - - - { - pairs.map((pair, i) => ( - - - - - - )) - } - -
-

Disease

- 		-

Drug

-
- {pair.disease.name} - {pair.disease.id} - - {pair.drug.name} - {pair.drug.id} -
- )} - - - - + + + +

Drug - Disease Pairs

+

+ These drug-disease pairs were generated using a machine learning model to align with the nodes + in the ROBOKOP knowledge graph. They highlight potential associations between various drugs and + a broad range of diseases, suggesting possible avenues for further research. These connections + can serve as a starting point for a new query by hovering over a pair and clicking “Start a Query”. +

+ +
+ + {isLoading ? 'Loading...' : ( + + + + + + + + + { + pairs.map((pair, i) => ( + + + + + + )) + } + +
+

Disease

+ 		+

Drug

+
+ {pair.disease.name} + {pair.disease.id} + + {pair.drug.name} + {pair.drug.id} +
+ )} + + + ); } From d55154760ed5f59ee2fb3e4869f0f21f982475ef Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 20 Aug 2024 10:58:37 -0400 Subject: [PATCH 04/17] increase font size --- src/pages/Explore.jsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/pages/Explore.jsx b/src/pages/Explore.jsx index 10def6eb..85ef8941 100644 --- a/src/pages/Explore.jsx +++ b/src/pages/Explore.jsx @@ -95,7 +95,7 @@ export default function Explore() {

Drug - Disease Pairs

-

+

These drug-disease pairs were generated using a machine learning model to align with the nodes in the ROBOKOP knowledge graph. They highlight potential associations between various drugs and a broad range of diseases, suggesting possible avenues for further research. These connections @@ -105,7 +105,7 @@ export default function Explore() {

{isLoading ? 'Loading...' : ( - +
+ @@ -128,6 +131,9 @@ export default function Explore() { {pair.drug.name} {pair.drug.id} + + ← View all datasets

Drug - Disease Pairs

These drug-disease pairs were generated using a machine learning model to align with the nodes @@ -102,6 +103,11 @@ export default function Explore() { can serve as a starting point for a new query by hovering over a pair and clicking “Start a Query”.

+

+ Scores with an asterisk and underline means the drug-disease pair is already known. The score is still + predicted using the trained model. +

+
{isLoading ? 'Loading...' : ( @@ -132,7 +138,15 @@ export default function Explore() { {pair.drug.id}+

Explore

+

+ Click a link below to view a curated dataset that can be further explored in the ROBOKOP query builder or answer explorer. +

+ +
+ + + Drug to Disease Pairs + +

+ These drug-disease pairs were generated using a machine learning model to align with the nodes + in the ROBOKOP knowledge graph. They highlight potential associations between various drugs and + a broad range of diseases, suggesting possible avenues for further research. These connections + can serve as a starting point for a new query by hovering over a pair and clicking “Start a Query”. +

+ + + + ); +} From 5e1166eb813647ac534c98ff73bc5901f9db7940 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 22 Oct 2024 11:07:58 -0400 Subject: [PATCH 09/17] add input fields --- src/pages/explore/DrugDiseasePairs.jsx | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/src/pages/explore/DrugDiseasePairs.jsx b/src/pages/explore/DrugDiseasePairs.jsx index 11963d4f..e0f99b62 100644 --- a/src/pages/explore/DrugDiseasePairs.jsx +++ b/src/pages/explore/DrugDiseasePairs.jsx @@ -1,4 +1,4 @@ -import { Button, makeStyles } from '@material-ui/core'; +import { Button, makeStyles, TextField } from '@material-ui/core'; import { ArrowRight } from '@material-ui/icons'; import React from 'react'; import { @@ -103,7 +103,7 @@ export default function DrugDiseasePairs() { can serve as a starting point for a new query by hovering over a pair and clicking “Start a Query”.

-

+

Scores with an asterisk and underline means the drug-disease pair is already known. The score is still predicted using the trained model.

@@ -113,15 +113,17 @@ export default function DrugDiseasePairs() { {isLoading ? 'Loading...' : (
From e3bce46999b81335c20f8f1577eef4303b129e68 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Mon, 21 Oct 2024 23:23:42 -0400 Subject: [PATCH 05/17] add data and script to reformat it --- api_routes/drug-disease.json | 5002 ----------------------- api_routes/routes.js | 2 +- data/drug-disease-mappings-subset.json | 1 + scripts/process-drug-disease-dataset.js | 48 + 4 files changed, 50 insertions(+), 5003 deletions(-) delete mode 100644 api_routes/drug-disease.json create mode 100644 data/drug-disease-mappings-subset.json create mode 100644 scripts/process-drug-disease-dataset.js diff --git a/api_routes/drug-disease.json b/api_routes/drug-disease.json deleted file mode 100644 index 79576fb5..00000000 --- a/api_routes/drug-disease.json +++ /dev/null @@ -1,5002 +0,0 @@ -[ - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0018616", - "name": "central serous chorioretinopathy" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0021667", - "name": "neuralgia" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "UMLS:C3854347", - "name": "Intentional product misuse" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "UMLS:C3805175", - "name": "Appendicolith" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0002203", - "name": "constipation disorder" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0043726", - "name": "multiple organ dysfunction syndrome" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0009688", - "name": "myasthenia gravis" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005113", - "name": "bacterial infectious disease" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0800175", - "name": "cardiogenic shock" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0000190", - "name": "ventricular fibrillation" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0017291", - "name": "reversible cerebral vasoconstriction syndrome" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005649", - "name": "appendicitis" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005298", - "name": "osteoporosis" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005420", - "name": "hypothyroidism" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005083", - "name": "psoriasis" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0003014", - "name": "rhinitis" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005441", - "name": "otitis media" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005709", - "name": "common cold" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005961", - "name": "sinusitis" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005108", - "name": "viral infectious disease" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0000740", - "name": "adenoid hypertrophy" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0004425", - "name": "hyperthyroidism" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005044", - "name": "hypertensive disorder" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005015", - "name": "diabetes mellitus" - } - }, - { - "drug": { - "id": "CHEBI:10082", - "name": "xylometazoline" - }, - "disease": { - "id": "MONDO:0005267", - "name": "heart disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0001358", - "name": "bronchial disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005146", - "name": "post-traumatic stress disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0006731", - "name": "drug-induced akathisia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "UMLS:C0001969", - "name": "Alcoholic Intoxication" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005383", - "name": "panic disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002025", - "name": "psychiatric disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005618", - "name": "anxiety disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0004681", - "name": "learning disability" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002494", - "name": "substance-related disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0007743", - "name": "attention deficit-hyperactivity disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0004456", - "name": "cocaine abuse" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005530", - "name": "opiate dependence" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002134", - "name": "physiological sexual disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0001106", - "name": "kidney failure" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0004985", - "name": "bipolar disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005567", - "name": "substance withdrawal syndrome" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005804", - "name": "hyperprolactinemia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0100192", - "name": "liver failure" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0007774", - "name": "hyperreflexia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0001286", - "name": "exotropia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "UMLS:C0011609", - "name": "Drug Eruptions" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005302", - "name": "attention deficit hyperactivity disorder, inattentive type" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0004985", - "name": "bipolar disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0022578", - "name": "childhood bladder carcinoma" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005105", - "name": "melanoma" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0006732", - "name": "drug-induced dyskinesia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005178", - "name": "osteoarthritis" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002009", - "name": "major depressive disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002032", - "name": "colon carcinoma" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0021063", - "name": "malignant colon neoplasm" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002277", - "name": "arteriosclerosis disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0007803", - "name": "multiple system atrophy" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005311", - "name": "atherosclerosis" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0011122", - "name": "obesity disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005146", - "name": "post-traumatic stress disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "UMLS:C0027055", - "name": "Myocardial Reperfusion Injury" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002909", - "name": "hyperglycemia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0007263", - "name": "cardiac rhythm disease" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005010", - "name": "coronary artery disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005148", - "name": "type 2 diabetes mellitus" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005466", - "name": "hypersomnia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005383", - "name": "panic disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005300", - "name": "chronic kidney disease" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005015", - "name": "diabetes mellitus" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005395", - "name": "movement disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "UMLS:C0525041", - "name": "Neurobehavioral Manifestations" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005302", - "name": "attention deficit hyperactivity disorder, inattentive type" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002342", - "name": "chondromalacia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005468", - "name": "hypotensive disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0004992", - "name": "cancer" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005091", - "name": "severe acute respiratory syndrome" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005047", - "name": "infertility disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0007743", - "name": "attention deficit-hyperactivity disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0007661", - "name": "Tourette syndrome" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0002909", - "name": "hyperglycemia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005192", - "name": "exocrine pancreatic carcinoma" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005362", - "name": "erectile dysfunction" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0000837", - "name": "bone resorption disease" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0018608", - "name": "pure autonomic failure" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0001384", - "name": "myopia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0007254", - "name": "breast cancer" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0000947", - "name": "psychosexual disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0009831", - "name": "malignant pancreatic neoplasm" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005043", - "name": "hyperplasia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0008903", - "name": "lung cancer" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0003709", - "name": "agoraphobia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005359", - "name": "drug-induced liver injury" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0000494", - "name": "renal fibrosis" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005362", - "name": "erectile dysfunction" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005072", - "name": "neuroblastoma" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0001247", - "name": "social phobia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005469", - "name": "orthostatic hypotension" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0000190", - "name": "ventricular fibrillation" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0001942", - "name": "generalized anxiety disorder" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0005180", - "name": "Parkinson disease" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - "id": "MONDO:0000437", - "name": "cerebellar ataxia" - } - }, - { - "drug": { - "id": "CHEBI:10093", - "name": "yohimbine" - }, - "disease": { - 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}, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0000736", - "name": "dyschromatosis universalis hereditaria" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0005279", - "name": "pulmonary embolism" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0005137", - "name": "nutritional disorder" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "UMLS:C0151547", - "name": "Cataract specified" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0005178", - "name": "osteoarthritis" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0005578", - "name": "arthritic joint disease" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0043303", - "name": "hyperacusis" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0001152", - "name": "amnestic disorder" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0004843", - "name": "pathologic nystagmus" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "UMLS:C0340464", - "name": "Premature Cardiac Complex" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0023557", - "name": "infective vaginitis" - } - }, - { - "drug": { - "id": "CHEBI:10102", - "name": "zaleplon" - }, - "disease": { - "id": "MONDO:0008698", - "name": "achalasia" - } - } -] \ No newline at end of file diff --git a/api_routes/routes.js b/api_routes/routes.js index 53dd100e..f00caf90 100644 --- a/api_routes/routes.js +++ b/api_routes/routes.js @@ -10,7 +10,7 @@ const services = require('./services'); const external_apis = require('./external'); const samples = JSON.parse(fs.readFileSync(path.join(__dirname, './sample-query-cache.json'))); -const drugDiseasePairs = JSON.parse(fs.readFileSync(path.join(__dirname, './drug-disease.json'))); +const drugDiseasePairs = JSON.parse(fs.readFileSync(path.join(__dirname, '../data/drug-disease-mappings-subset.json'))).slice(0, 500); router.use('/', external_apis); diff --git a/data/drug-disease-mappings-subset.json b/data/drug-disease-mappings-subset.json new file mode 100644 index 00000000..0353674e --- /dev/null +++ b/data/drug-disease-mappings-subset.json @@ -0,0 +1 @@ +[{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9998655319,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0005178","name":"osteoarthritis"},"score":0.9998351336,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin 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acid"},"disease":{"id":"MONDO:0004277","name":"gonorrhea"},"score":0.5000641942,"known":false},{"drug":{"id":"CHEBI:3732","name":"clarithromycin"},"disease":{"id":"MONDO:0017409","name":"fetal cytomegalovirus syndrome"},"score":0.5000575185,"known":false},{"drug":{"id":"CHEBI:28939","name":"acetylcysteine"},"disease":{"id":"MONDO:0001797","name":"chancroid"},"score":0.5000517964,"known":false},{"drug":{"id":"UNII:T4H8FMA7IM","name":"siltuximab"},"disease":{"id":"MONDO:0007576","name":"esophageal cancer"},"score":0.5000382662,"known":false},{"drug":{"id":"CHEBI:15428","name":"glycine"},"disease":{"id":"MONDO:0006733","name":"dry eye syndrome"},"score":0.5000302196,"known":false},{"drug":{"id":"UNII:PP0SHH6V16","name":"alirocumab"},"disease":{"id":"HP:0000969","name":"edema"},"score":0.5000221133,"known":false},{"drug":{"id":"CHEBI:31182","name":"alacepril"},"disease":{"id":"MONDO:0001461","name":"tinea corporis"},"score":0.5000206232,"known":false},{"drug":{"id":"PUBCHEM.COMPOUND:5199","name":"sennosides"},"disease":{"id":"MONDO:0005972","name":"streptococcal pneumonia"},"score":0.5000194311,"known":false},{"drug":{"id":"CHEBI:47780","name":"clomipramine"},"disease":{"id":"MONDO:0006733","name":"dry eye syndrome"},"score":0.5000162125,"known":false}] \ No newline at end of file diff --git a/scripts/process-drug-disease-dataset.js b/scripts/process-drug-disease-dataset.js new file mode 100644 index 00000000..c4da75dd --- /dev/null +++ b/scripts/process-drug-disease-dataset.js @@ -0,0 +1,48 @@ +/* eslint-disable no-restricted-syntax */ +const fs = require('fs'); +const path = require('path'); + +const input = '../data/raw/DrugtoDiseasePrediction-subset.json'; +const output = '../data/drug-disease-mappings-subset.json'; +const lowerScoreLimit = 0.5; +const prettyPrintJson = false; + +const rawMaps = JSON.parse( + fs.readFileSync(path.resolve(__dirname, input), 'utf-8'), +); + +/** + * @typedef {{ + * id: string, + * name: string, + * }} Node + * + * @typedef {{ + * drug: Node, + * disease: Node, + * score: number, + * known: boolean, + * }} DrugDiseaseMapping + * + * @type {DrugDiseaseMapping[]} + */ +const arrayOfMappings = Object.entries(rawMaps.Score) + .filter(([, score]) => score >= lowerScoreLimit) + .sort((a, b) => b[1] - a[1]) + .map(([id, score]) => ({ + drug: { + id: rawMaps.DrugID[id], + name: rawMaps.DrugName[id], + }, + disease: { + id: rawMaps.DiseaseID[id], + name: rawMaps.DiseaseName[id], + }, + score, + known: rawMaps.Known[id] === '1', + })); + +fs.writeFileSync( + path.resolve(__dirname, output), + JSON.stringify(arrayOfMappings, null, prettyPrintJson ? 2 : 0), +); From fc3c40888e5c7207738d2ac9e3739b05b9bed045 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Mon, 21 Oct 2024 23:25:57 -0400 Subject: [PATCH 06/17] add score to table --- src/pages/Explore.jsx | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/pages/Explore.jsx b/src/pages/Explore.jsx index 85ef8941..d0b7403e 100644 --- a/src/pages/Explore.jsx +++ b/src/pages/Explore.jsx @@ -114,6 +114,9 @@ export default function Explore() {

Drug

 +

Score

+
+ {pair.score.toFixed(6)} + - {pair.score.toFixed(6)} + {pair.score.toFixed(6)}{pair.known ? * : null}
- {pair.score.toFixed(6)}{pair.known ? * : null} + { + pair.known ? ( + + {pair.score.toFixed(6)}* + + ) : ( + pair.score.toFixed(6) + ) + }
- - + - - From 4a00474f9f84867a3dc969ce9a460aa4cd113ab3 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 22 Oct 2024 11:10:20 -0400 Subject: [PATCH 10/17] fix lint --- src/pages/explore/DrugDiseasePairs.jsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pages/explore/DrugDiseasePairs.jsx b/src/pages/explore/DrugDiseasePairs.jsx index e0f99b62..a93226ce 100644 --- a/src/pages/explore/DrugDiseasePairs.jsx +++ b/src/pages/explore/DrugDiseasePairs.jsx @@ -1,4 +1,4 @@ -import { Button, makeStyles, TextField } from '@material-ui/core'; +import { Button, makeStyles } from '@material-ui/core'; import { ArrowRight } from '@material-ui/icons'; import React from 'react'; import { From fe270653f36237db039300020653fb02009c5a3c Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 22 Oct 2024 11:14:41 -0400 Subject: [PATCH 11/17] use base proxy --- src/pages/explore/DrugDiseasePairs.jsx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/pages/explore/DrugDiseasePairs.jsx b/src/pages/explore/DrugDiseasePairs.jsx index a93226ce..5a753ff6 100644 --- a/src/pages/explore/DrugDiseasePairs.jsx +++ b/src/pages/explore/DrugDiseasePairs.jsx @@ -7,6 +7,7 @@ import { import { useHistory, Link } from 'react-router-dom'; import QueryBuilderContext from '~/context/queryBuilder'; import useQueryBuilder from '../queryBuilder/useQueryBuilder'; +import { api } from '../../API/baseUrlProxy'; const useStyles = makeStyles({ hover: { @@ -20,9 +21,8 @@ const useStyles = makeStyles({ }); const fetchPairs = async () => { - const res = await fetch('/api/explore', { method: 'POST' }); - if (!res.ok) throw new Error(res.statusText); - return res.json(); + const res = await api.post('/api/explore'); + return res.data; }; export default function DrugDiseasePairs() { From a8d6e55f836aeb17feda3ac324da4c36830c4a0c Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 22 Oct 2024 11:29:59 -0400 Subject: [PATCH 12/17] move drugChemicalPair fetcher --- src/API/explorePage.js | 16 ++++++++++++++++ src/pages/explore/DrugDiseasePairs.jsx | 7 ++----- 2 files changed, 18 insertions(+), 5 deletions(-) create mode 100644 src/API/explorePage.js diff --git a/src/API/explorePage.js b/src/API/explorePage.js new file mode 100644 index 00000000..a6efc13f --- /dev/null +++ b/src/API/explorePage.js @@ -0,0 +1,16 @@ +import utils from './utils'; +import { api } from './baseUrlProxy'; + +const routes = { + async getDrugChemicalPairs() { + let response; + try { + response = await api.post('/api/explore'); + } catch (error) { + return utils.handleAxiosError(error); + } + return response.data; + }, +}; + +export default routes; diff --git a/src/pages/explore/DrugDiseasePairs.jsx b/src/pages/explore/DrugDiseasePairs.jsx index 5a753ff6..0eb1336c 100644 --- a/src/pages/explore/DrugDiseasePairs.jsx +++ b/src/pages/explore/DrugDiseasePairs.jsx @@ -7,7 +7,7 @@ import { import { useHistory, Link } from 'react-router-dom'; import QueryBuilderContext from '~/context/queryBuilder'; import useQueryBuilder from '../queryBuilder/useQueryBuilder'; -import { api } from '../../API/baseUrlProxy'; +import explorePage from '~/API/explorePage'; const useStyles = makeStyles({ hover: { @@ -20,10 +20,7 @@ const useStyles = makeStyles({ }, }); -const fetchPairs = async () => { - const res = await api.post('/api/explore'); - return res.data; -}; +const fetchPairs = explorePage.getDrugChemicalPairs; export default function DrugDiseasePairs() { const [pairs, setPairs] = React.useState([]); From 34a9ed91da15befbbcf4486914e37178d9e3a979 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Sun, 10 Nov 2024 21:53:30 -0500 Subject: [PATCH 13/17] restructure explore db code --- data/explore.db | 0 explore/README.md | 0 explore/db_utils.js | 29 ++++++++++++ explore/query/drug-disease.js | 30 +++++++++++++ explore/scripts/init-drug-disease.js | 66 ++++++++++++++++++++++++++++ 5 files changed, 125 insertions(+) create mode 100644 data/explore.db create mode 100644 explore/README.md create mode 100644 explore/db_utils.js create mode 100644 explore/query/drug-disease.js create mode 100644 explore/scripts/init-drug-disease.js diff --git a/data/explore.db b/data/explore.db new file mode 100644 index 00000000..e69de29b diff --git a/explore/README.md b/explore/README.md new file mode 100644 index 00000000..e69de29b diff --git a/explore/db_utils.js b/explore/db_utils.js new file mode 100644 index 00000000..db22ade5 --- /dev/null +++ b/explore/db_utils.js @@ -0,0 +1,29 @@ +const run = async (db, sql, params) => new Promise((res, rej) => { + db.run(sql, params, (err) => { + if (err) rej(err); + else res(); + }); +}); + +const all = async (db, sql, params) => new Promise((res, rej) => { + db.all(sql, params, (err, rows) => { + if (err) rej(err); + else res(rows); + }); +}); + +/** + * Same as normal template literal but 'sql' tag allows syntax highlighting in editor + */ +const sql = (strings, ...args) => strings.reduce((str, curr, i) => str + curr + (args[i] || ''), ''); + +module.exports = { + /** + * Promise-based wrappers for node-sqlite3. Attempts to mirror API, first param is db instance + */ + db_p: { + run, + all, + }, + sql, +}; diff --git a/explore/query/drug-disease.js b/explore/query/drug-disease.js new file mode 100644 index 00000000..1c725af4 --- /dev/null +++ b/explore/query/drug-disease.js @@ -0,0 +1,30 @@ +const path = require('path'); +const sqlite3 = require('sqlite3'); +const { db_p, sql } = require('../db_utils'); + +require('dotenv').config({ path: path.resolve(__dirname, '../../.env') }); + +const db = new sqlite3.Database(process.env.EXPLORE_DB); + +(async () => { + const t0 = performance.now(); + + let rows; + try { + rows = await db_p.all( + db, + sql` + SELECT * FROM drug_disease_pairs + WHERE disease_name = "sneeze" + ORDER BY score DESC + LIMIT 5 OFFSET 5 + ` + ); + } catch (err) { + console.error(rows); + } + + console.log(rows); + + console.log(performance.now() - t0); +})(); diff --git a/explore/scripts/init-drug-disease.js b/explore/scripts/init-drug-disease.js new file mode 100644 index 00000000..b1f62965 --- /dev/null +++ b/explore/scripts/init-drug-disease.js @@ -0,0 +1,66 @@ +/* eslint-disable no-continue */ +/* eslint-disable no-console */ +/* eslint-disable no-restricted-syntax */ + +const fs = require('fs'); +const path = require('path'); +const sqlite3 = require('sqlite3'); +const { db_p, sql } = require('../db_utils'); + +require('dotenv').config({ path: path.resolve(__dirname, '../../.env') }); + +const input = '../data/raw/DrugtoDiseasePrediction-full-9-30-24.json'; +const lowerScoreLimit = 0.5; + +const db = new sqlite3.Database(process.env.EXPLORE_DB); + +(async () => { + await db_p.run(db, sql` + CREATE TABLE IF NOT EXISTS drug_disease_pairs ( + drug_name TEXT NOT NULL, + drug_id TEXT NOT NULL, + disease_name TEXT NOT NULL, + disease_id TEXT NOT NULL, + score REAL NOT NULL, + known BOOLEAN NOT NULL CHECK (known IN (0, 1)) + ) + `); + await db_p.run(db, sql`DELETE FROM drug_disease_pairs`); + + const rawMaps = JSON.parse( + fs.readFileSync(path.resolve(__dirname, input), 'utf-8'), + ); + + await db_p.run(db, sql`BEGIN TRANSACTION`); + for (const [id, score] of Object.entries(rawMaps.Score).sort((a, b) => b[1] - a[1])) { + if (score < lowerScoreLimit) continue; + + const drug = { + id: rawMaps.DrugID[id], + name: rawMaps.DrugName[id], + }; + const disease = { + id: rawMaps.DiseaseID[id], + name: rawMaps.DiseaseName[id], + }; + const known = rawMaps.Known[id] === '1'; + + const command = sql`INSERT INTO drug_disease_pairs VALUES (?, ?, ?, ?, ?, ?)`; + const params = [ + drug.name, + drug.id, + disease.name, + disease.id, + score, + known ? '1' : '0', + ]; + + try { + db_p.run(db, command, params); + } catch (err) { + console.error('Error:', err, 'Params:', params); + } + } + + await db_p.run(db, sql`COMMIT`); +})(); From 836cbc169c80b104eb43980f368f088cf81b8acd Mon Sep 17 00:00:00 2001 From: David Glymph Date: Sun, 10 Nov 2024 21:54:08 -0500 Subject: [PATCH 14/17] remove old explore route code --- api_routes/routes.js | 9 +- data/drug-disease-mappings-subset.json | 1 - data/explore.db | 0 explore/query/drug-disease.js | 2 +- package-lock.json | 1298 +++++++++++++++++++++-- package.json | 3 +- scripts/process-drug-disease-dataset.js | 48 - 7 files changed, 1227 insertions(+), 134 deletions(-) delete mode 100644 data/drug-disease-mappings-subset.json delete mode 100644 data/explore.db delete mode 100644 scripts/process-drug-disease-dataset.js diff --git a/api_routes/routes.js b/api_routes/routes.js index 3cef6424..5564dded 100644 --- a/api_routes/routes.js +++ b/api_routes/routes.js @@ -10,7 +10,6 @@ const services = require('./services'); const external_apis = require('./external'); const samples = JSON.parse(fs.readFileSync(path.join(__dirname, './sample-query-cache.json'))); -const drugDiseasePairs = JSON.parse(fs.readFileSync(path.join(__dirname, '../data/drug-disease-mappings-subset.json'))).slice(0, 1000); router.use('/', external_apis); @@ -59,10 +58,10 @@ router.route('/quick_answer') } }); -router.route('/explore') - .post(async (req, res) => { - res.status(200).send(drugDiseasePairs); - }); +// router.route('/explore') +// .post(async (req, res) => { +// res.status(200).send(drugDiseasePairs); +// }); router.route('/answer') .post(async (req, res) => { diff --git a/data/drug-disease-mappings-subset.json b/data/drug-disease-mappings-subset.json deleted file mode 100644 index 0353674e..00000000 --- a/data/drug-disease-mappings-subset.json +++ /dev/null @@ -1 +0,0 @@ -[{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9998655319,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0005178","name":"osteoarthritis"},"score":0.9998351336,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0005109","name":"hiv infectious disease"},"score":0.9998150468,"known":false},{"drug":{"id":"CHEBI:2682","name":"amphotericin b"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9998025894,"known":false},{"drug":{"id":"CHEBI:5108","name":"fluocinolone acetonide"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9997792244,"known":false},{"drug":{"id":"CHEBI:2682","name":"amphotericin b"},"disease":{"id":"MONDO:0005178","name":"osteoarthritis"},"score":0.9997580647,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"HP:0001742","name":"nasal congestion"},"score":0.9997442961,"known":false},{"drug":{"id":"CHEBI:5108","name":"fluocinolone acetonide"},"disease":{"id":"MONDO:0005178","name":"osteoarthritis"},"score":0.9997293949,"known":false},{"drug":{"id":"CHEBI:2682","name":"amphotericin b"},"disease":{"id":"MONDO:0005109","name":"hiv infectious disease"},"score":0.9997285604,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0005754","name":"epilepsy with generalized tonic-clonic seizures"},"score":0.9997004271,"known":false},{"drug":{"id":"CHEBI:5108","name":"fluocinolone acetonide"},"disease":{"id":"MONDO:0005109","name":"hiv infectious disease"},"score":0.9996963739,"known":false},{"drug":{"id":"CHEBI:8378","name":"prednisolone"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9996470809,"known":false},{"drug":{"id":"CHEBI:29007","name":"ceftriaxone"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9996420741,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"HP:0031417","name":"rhinorrhea"},"score":0.9996400476,"known":false},{"drug":{"id":"CHEBI:2682","name":"amphotericin b"},"disease":{"id":"HP:0001742","name":"nasal congestion"},"score":0.9996246696,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"HP:0000989","name":"pruritus"},"score":0.9996225834,"known":false},{"drug":{"id":"CHEBI:9667","name":"triamcinolone"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9995808601,"known":false},{"drug":{"id":"CHEBI:5108","name":"fluocinolone acetonide"},"disease":{"id":"HP:0001742","name":"nasal congestion"},"score":0.9995802045,"known":false},{"drug":{"id":"CHEBI:8378","name":"prednisolone"},"disease":{"id":"MONDO:0005178","name":"osteoarthritis"},"score":0.9995674491,"known":false},{"drug":{"id":"CHEBI:29007","name":"ceftriaxone"},"disease":{"id":"MONDO:0005178","name":"osteoarthritis"},"score":0.9995613098,"known":false},{"drug":{"id":"CHEBI:2682","name":"amphotericin b"},"disease":{"id":"MONDO:0005754","name":"epilepsy with generalized tonic-clonic seizures"},"score":0.9995603561,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0004980","name":"atopic eczema"},"score":0.9995363951,"known":false},{"drug":{"id":"CHEBI:8382","name":"prednisone"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9995247126,"known":false},{"drug":{"id":"CHEBI:8232","name":"piperacillin"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9995217919,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0005277","name":"migraine disorder"},"score":0.9995214343,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"MONDO:0003014","name":"rhinitis"},"score":0.9995177984,"known":false},{"drug":{"id":"CHEBI:8378","name":"prednisolone"},"disease":{"id":"MONDO:0005109","name":"hiv infectious disease"},"score":0.9995147586,"known":false},{"drug":{"id":"CHEBI:5108","name":"fluocinolone acetonide"},"disease":{"id":"MONDO:0005754","name":"epilepsy with generalized tonic-clonic seizures"},"score":0.9995082021,"known":false},{"drug":{"id":"CHEBI:29007","name":"ceftriaxone"},"disease":{"id":"MONDO:0005109","name":"hiv infectious disease"},"score":0.9995078444,"known":false},{"drug":{"id":"CHEBI:28001","name":"vancomycin"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9995054603,"known":false},{"drug":{"id":"CHEBI:17334","name":"penicillin g"},"disease":{"id":"HP:0003124","name":"hypercholesterolemia"},"score":0.9995023012,"known":false},{"drug":{"id":"CHEBI:3897","name":"cortisone"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes mellitus"},"score":0.9994885325,"known":false},{"drug":{"id":"CHEBI:9667","name":"triamcinolone"},"disease":{"id":"MONDO:0005178","name":"osteoarthritis"},"score":0.9994863272,"known":false},{"drug":{"id":"CHEBI:2682","name":"amphotericin b"},"disease":{"id":"HP:0031417","name":"rhinorrhea"},"score":0.9994717836,"known":false},{"drug":{"id":"CHEBI:2682","name":"amphotericin b"},"disease":{"id":"HP:0000989","name":"pruritus"},"score":0.999446094,"known":false},{"drug":{"id":"PUBCHEM.COMPOUND:54671203","name":"doxycycline"},"disease":{"id":"MONDO:0005148","name":"type 2 diabetes 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@@ -27487,7 +28598,7 @@ "version": "2.0.2", "resolved": "https://registry.npmjs.org/unique-slug/-/unique-slug-2.0.2.tgz", "integrity": "sha512-zoWr9ObaxALD3DOPfjPSqxt4fnZiWblxHIgeWqW8x7UqDzEtHEQLzji2cuJYQFCU6KmoJikOYAZlrTHHebjx2w==", - "dev": true, + "devOptional": true, "dependencies": { "imurmurhash": "^0.1.4" } @@ -27843,10 +28954,14 @@ } }, "node_modules/uuid": { - "version": "2.0.3", - "resolved": "https://registry.npmjs.org/uuid/-/uuid-2.0.3.tgz", - "integrity": "sha1-Z+LoY3lyFVMN/zGOW/nc6/1Hsho=", - "deprecated": "Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details." + "version": "8.3.2", + "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz", + "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==", + "license": "MIT", + "peer": true, + "bin": { + "uuid": "dist/bin/uuid" + } }, "node_modules/v8-compile-cache": { "version": "2.1.1", @@ -27940,10 +29055,20 @@ "vis-util": "^1.1.6" } }, - "node_modules/vis-util": { + "node_modules/vis-network/node_modules/moment": { + "version": "2.24.0", + "resolved": "https://registry.npmjs.org/moment/-/moment-2.24.0.tgz", + "integrity": "sha512-bV7f+6l2QigeBBZSM/6yTNq4P2fNpSWj/0e7jQcy87A8e7o2nAfP/34/2ky5Vw4B9S446EtIhodAzkFCcR4dQg==", + "license": "MIT", + "engines": { + "node": "*" + } + }, + "node_modules/vis-network/node_modules/vis-util": { "version": "1.1.10", "resolved": "https://registry.npmjs.org/vis-util/-/vis-util-1.1.10.tgz", "integrity": "sha512-8hGSxsFi2ogYYweClQyITzWnirWgQ8p0i9M4d3OXMuUO8vjXrf+2zHOYI9OZbtUduxAWuMEePnS9BXDtPJmJ7Q==", + "license": "(Apache-2.0 OR MIT)", "dependencies": { "moment": "2.24.0", "vis-uuid": "1.1.3" @@ -27956,12 +29081,18 @@ "url": "https://opencollective.com/visjs" } }, - "node_modules/vis-util/node_modules/moment": { - "version": "2.24.0", - "resolved": "https://registry.npmjs.org/moment/-/moment-2.24.0.tgz", - "integrity": "sha512-bV7f+6l2QigeBBZSM/6yTNq4P2fNpSWj/0e7jQcy87A8e7o2nAfP/34/2ky5Vw4B9S446EtIhodAzkFCcR4dQg==", + "node_modules/vis-util": { + "version": "4.3.4", + "resolved": "https://registry.npmjs.org/vis-util/-/vis-util-4.3.4.tgz", + "integrity": "sha512-hJIZNrwf4ML7FYjs+m+zjJfaNvhjk3/1hbMdQZVnwwpOFJS/8dMG8rdbOHXcKoIEM6U5VOh3HNpaDXxGkOZGpw==", + "license": "(Apache-2.0 OR MIT)", + "peer": true, "engines": { - "node": "*" + "node": ">=8" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/visjs" } }, "node_modules/vis-uuid": { @@ -27969,6 +29100,7 @@ "resolved": "https://registry.npmjs.org/vis-uuid/-/vis-uuid-1.1.3.tgz", "integrity": "sha512-2B6XdY1bkzbUh+TugmnAaFa61KO9R5pzBzIuFIm8a9FrkbxIdSmQXV+FbfkL8QunkQV/bT0JDLQ2puqCS2+0Og==", "deprecated": "We don't use this library anymore so you shouldn't either. Use e.g. 'uuid' instead!", + "license": "(Apache-2.0 OR MIT)", "engines": { "node": ">=8" } @@ -28691,6 +29823,16 @@ "integrity": "sha1-2e8H3Od7mQK4o6j6SzHD4/fm6Ho=", "dev": true }, + "node_modules/wide-align": { + "version": "1.1.5", + "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.5.tgz", + "integrity": "sha512-eDMORYaPNZ4sQIuuYPDHdQvf4gyCF9rEEV/yPxGfwPkRodwEgiMUUXTx/dex+Me0wxx53S+NgUHaP7y3MGlDmg==", + "license": "ISC", + "optional": true, + "dependencies": { + "string-width": "^1.0.2 || 2 || 3 || 4" + } + }, "node_modules/widest-line": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/widest-line/-/widest-line-3.1.0.tgz", diff --git a/package.json b/package.json index b09a292b..ea095050 100644 --- a/package.json +++ b/package.json @@ -88,7 +88,8 @@ "react-widgets": "^4.5.0", "regenerator-runtime": "^0.13.7", "shortid": "^2.2.15", - "slugify": "^1.4.5" + "slugify": "^1.4.5", + "sqlite3": "^5.1.7" }, "scripts": { "start": "webpack --mode=development --config webpack.dev.js && nodemon server.js", diff --git a/scripts/process-drug-disease-dataset.js b/scripts/process-drug-disease-dataset.js deleted file mode 100644 index c4da75dd..00000000 --- a/scripts/process-drug-disease-dataset.js +++ /dev/null @@ -1,48 +0,0 @@ -/* eslint-disable no-restricted-syntax */ -const fs = require('fs'); -const path = require('path'); - -const input = '../data/raw/DrugtoDiseasePrediction-subset.json'; -const output = '../data/drug-disease-mappings-subset.json'; -const lowerScoreLimit = 0.5; -const prettyPrintJson = false; - -const rawMaps = JSON.parse( - fs.readFileSync(path.resolve(__dirname, input), 'utf-8'), -); - -/** - * @typedef {{ - * id: string, - * name: string, - * }} Node - * - * @typedef {{ - * drug: Node, - * disease: Node, - * score: number, - * known: boolean, - * }} DrugDiseaseMapping - * - * @type {DrugDiseaseMapping[]} - */ -const arrayOfMappings = Object.entries(rawMaps.Score) - .filter(([, score]) => score >= lowerScoreLimit) - .sort((a, b) => b[1] - a[1]) - .map(([id, score]) => ({ - drug: { - id: rawMaps.DrugID[id], - name: rawMaps.DrugName[id], - }, - disease: { - id: rawMaps.DiseaseID[id], - name: rawMaps.DiseaseName[id], - }, - score, - known: rawMaps.Known[id] === '1', - })); - -fs.writeFileSync( - path.resolve(__dirname, output), - JSON.stringify(arrayOfMappings, null, prettyPrintJson ? 2 : 0), -); From 595e288e27294a30ad95ebac245af455e50f4d89 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Sun, 10 Nov 2024 23:48:30 -0500 Subject: [PATCH 15/17] drug disease pairs db query method --- explore/db_utils.js | 8 ++ explore/query/drug-disease.js | 141 +++++++++++++++++++++++++++++----- 2 files changed, 130 insertions(+), 19 deletions(-) diff --git a/explore/db_utils.js b/explore/db_utils.js index db22ade5..c51413b4 100644 --- a/explore/db_utils.js +++ b/explore/db_utils.js @@ -5,6 +5,13 @@ const run = async (db, sql, params) => new Promise((res, rej) => { }); }); +const get = async (db, sql, params) => new Promise((res, rej) => { + db.get(sql, params, (err, row) => { + if (err) rej(err); + else res(row); + }); +}); + const all = async (db, sql, params) => new Promise((res, rej) => { db.all(sql, params, (err, rows) => { if (err) rej(err); @@ -23,6 +30,7 @@ module.exports = { */ db_p: { run, + get, all, }, sql, diff --git a/explore/query/drug-disease.js b/explore/query/drug-disease.js index ef13524e..5b75fe73 100644 --- a/explore/query/drug-disease.js +++ b/explore/query/drug-disease.js @@ -1,3 +1,5 @@ +/* eslint-disable no-restricted-syntax */ +/* eslint-disable no-use-before-define */ const path = require('path'); const sqlite3 = require('sqlite3'); const { db_p, sql } = require('../db_utils'); @@ -6,25 +8,126 @@ require('dotenv').config({ path: path.resolve(__dirname, '../../.env') }); const db = new sqlite3.Database(process.env.EXPLORE_DB); -(async () => { - const t0 = performance.now(); - - let rows; - try { - rows = await db_p.all( - db, - sql` - SELECT * FROM drug_disease_pairs - WHERE disease_name = "sneeze" - ORDER BY score DESC - LIMIT 5 OFFSET 5 - `, - ); - } catch (err) { - console.error(rows); +/** + * @param {{ + * sort?: { + * drug_name?: "asc" | "desc", + * disease_name?: "asc" | "desc", + * score?: "asc" | "desc", + * known?: "asc" | "desc", + * } + * filters?: { + * drug_name?: string, + * drug_id?: string, + * disease_name?: string, + * disease_id?: string, + * }, + * pagination: { + * limit: number, + * offset: number, + * } + * }} params + * @returns {Promise<{ + * rows: { + * drug_name: string, + * drug_id: string, + * disease_name: string, + * disease_id: string, + * score: number, + * known: number + * }[], + * num_of_results: number, + * limit: number, + * offset: number, + * }>} + */ +async function getDrugDiseasePairs({ sort, filters, pagination }) { + const { whereClause, whereParams } = buildWhereClause(filters); + const orderByClause = buildOrderByClause(sort); + + const { paginationClause, paginationParams } = buildPaginationClause(pagination.limit, pagination.offset); + + const params = [...whereParams, ...paginationParams]; + + const query = sql`\ + SELECT * FROM drug_disease_pairs${whereClause}${orderByClause}${paginationClause}\ + `; + const countQuery = sql`\ + SELECT COUNT(*) AS total FROM drug_disease_pairs${whereClause}\ + `; + + return new Promise((resolve, reject) => { + db.parallelize(() => { + Promise.all([ + db_p.all(db, query, params), + db_p.get(db, countQuery, whereParams), + ]) + .then(([rows, { total }]) => { + resolve({ + rows, + num_of_results: total, + ...pagination, + }); + }) + .catch(reject); + }); + }); +} + +function buildWhereClause(filters) { + const whereClauses = []; + const params = []; + + if (filters) { + if (filters.drug_name) { + whereClauses.push('drug_name LIKE ?'); + params.push(`%${filters.drug_name}%`); + } + if (filters.drug_id) { + whereClauses.push('drug_id LIKE ?'); + params.push(`%${filters.drug_id}%`); + } + if (filters.disease_name) { + whereClauses.push('disease_name LIKE ?'); + params.push(`%${filters.disease_name}%`); + } + if (filters.disease_id) { + whereClauses.push('disease_id LIKE ?'); + params.push(`%${filters.disease_id}%`); + } + } + + const whereClause = + (whereClauses.length > 0 ? ` WHERE ${whereClauses.join(' AND ')}` : ''); + return { whereClause, whereParams: params }; +} + +function buildOrderByClause(sort) { + let orderByClause = ''; + if (sort) { + const orderClauses = []; + for (const [column, direction] of Object.entries(sort)) { + if ( + ['drug_name', 'disease_name', 'score', 'known'].includes(column) && + ['asc', 'desc'].includes(direction) + ) { + orderClauses.push(`${column} ${direction.toUpperCase()}`); + } + } + if (orderClauses.length > 0) { + orderByClause += ` ORDER BY ${orderClauses.join(', ')}`; + } } + return orderByClause; +} - console.log(rows); +function buildPaginationClause(limit, offset) { + return { + paginationClause: ' LIMIT ? OFFSET ?', + paginationParams: [limit, offset], + }; +} - console.log(performance.now() - t0); -})(); +module.exports = { + getDrugDiseasePairs, +}; From 1c05676f048f2ba4880f0c989b670089c410f1e8 Mon Sep 17 00:00:00 2001 From: David Glymph Date: Mon, 11 Nov 2024 00:10:01 -0500 Subject: [PATCH 16/17] drug-disease route handler --- api_routes/routes.js | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/api_routes/routes.js b/api_routes/routes.js index 5564dded..01ca60dd 100644 --- a/api_routes/routes.js +++ b/api_routes/routes.js @@ -9,6 +9,8 @@ const { handleAxiosError } = require('./utils'); const services = require('./services'); const external_apis = require('./external'); +const { getDrugDiseasePairs } = require('../explore/query/drug-disease'); + const samples = JSON.parse(fs.readFileSync(path.join(__dirname, './sample-query-cache.json'))); router.use('/', external_apis); @@ -58,10 +60,24 @@ router.route('/quick_answer') } }); -// router.route('/explore') -// .post(async (req, res) => { -// res.status(200).send(drugDiseasePairs); -// }); +router.route('/explore/drug-disease') + .post(async (req, res) => { + const { sort, filters, pagination } = req.body; + + if (!pagination || !Number.isInteger(pagination.offset) || !Number.isInteger(pagination.limit)) return res.status(400).json({ error: 'Missing pagination' }); + if (pagination.limit < 1 || pagination.offset < 0) return res.status(400).json({ error: 'Invalid limit or offset value' }); + + const limit = Math.min(pagination.limit, 500); + const { offset } = pagination; + + try { + const results = await getDrugDiseasePairs({ sort, filters, pagination: { limit, offset } }); + return res.status(200).json(results); + } catch (error) { + console.error('Error in explore page query:', error, req.body); + return res.status(500).json({ error: 'Internal server error' }); + } + }); router.route('/answer') .post(async (req, res) => { From cc6ca1f489816e2cc82221586e3fd609898ac00d Mon Sep 17 00:00:00 2001 From: David Glymph Date: Tue, 26 Nov 2024 09:44:36 -0500 Subject: [PATCH 17/17] update UI to work with new API --- package-lock.json | 34 ++++++++++++++++++++++++++ package.json | 1 + src/API/explorePage.js | 12 +++++++-- src/components/Table.jsx | 7 ++++++ src/pages/explore/DrugDiseasePairs.jsx | 8 +++--- 5 files changed, 56 insertions(+), 6 deletions(-) create mode 100644 src/components/Table.jsx diff --git a/package-lock.json b/package-lock.json index 5cf97406..b6d7c3ea 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,6 +14,7 @@ "@material-ui/data-grid": "^4.0.0-alpha.2", "@material-ui/icons": "^4.9.1", "@material-ui/lab": "^4.0.0-alpha.56", + "@tanstack/react-table": "^8.20.5", "ag-grid-community": "^23.2.1", "ag-grid-react": "^23.2.1", "axios": "^0.21.1", @@ -5940,6 +5941,39 @@ "node": ">=6" } }, + "node_modules/@tanstack/react-table": { + "version": "8.20.5", + "resolved": "https://registry.npmjs.org/@tanstack/react-table/-/react-table-8.20.5.tgz", + "integrity": "sha512-WEHopKw3znbUZ61s9i0+i9g8drmDo6asTWbrQh8Us63DAk/M0FkmIqERew6P71HI75ksZ2Pxyuf4vvKh9rAkiA==", + "license": "MIT", + "dependencies": { + "@tanstack/table-core": "8.20.5" + }, + "engines": { + "node": ">=12" + }, + "funding": { + "type": "github", + "url": "https://github.com/sponsors/tannerlinsley" + }, + "peerDependencies": { + "react": ">=16.8", + "react-dom": ">=16.8" + } + }, + "node_modules/@tanstack/table-core": { + "version": "8.20.5", + "resolved": "https://registry.npmjs.org/@tanstack/table-core/-/table-core-8.20.5.tgz", + "integrity": "sha512-P9dF7XbibHph2PFRz8gfBKEXEY/HJPOhym8CHmjF8y3q5mWpKx9xtZapXQUWCgkqvsK0R46Azuz+VaxD4Xl+Tg==", + "license": "MIT", + "engines": { + "node": ">=12" + }, + "funding": { + "type": "github", + "url": "https://github.com/sponsors/tannerlinsley" + } + }, "node_modules/@testing-library/dom": { "version": "7.26.5", "resolved": "https://registry.npmjs.org/@testing-library/dom/-/dom-7.26.5.tgz", diff --git a/package.json b/package.json index ea095050..2b9b395e 100644 --- a/package.json +++ b/package.json @@ -50,6 +50,7 @@ "@material-ui/data-grid": "^4.0.0-alpha.2", "@material-ui/icons": "^4.9.1", "@material-ui/lab": "^4.0.0-alpha.56", + "@tanstack/react-table": "^8.20.5", "ag-grid-community": "^23.2.1", "ag-grid-react": "^23.2.1", "axios": "^0.21.1", diff --git a/src/API/explorePage.js b/src/API/explorePage.js index a6efc13f..08c4094b 100644 --- a/src/API/explorePage.js +++ b/src/API/explorePage.js @@ -5,11 +5,19 @@ const routes = { async getDrugChemicalPairs() { let response; try { - response = await api.post('/api/explore'); + response = await api.post( + '/api/explore/drug-disease', + { + pagination: { + offset: 0, + limit: 1000, + }, + }, + ); } catch (error) { return utils.handleAxiosError(error); } - return response.data; + return response.data.rows; }, }; diff --git a/src/components/Table.jsx b/src/components/Table.jsx new file mode 100644 index 00000000..006dabe2 --- /dev/null +++ b/src/components/Table.jsx @@ -0,0 +1,7 @@ +import React from 'react'; + +// drug_name + +export default function Table() { + return
Hello
; +} diff --git a/src/pages/explore/DrugDiseasePairs.jsx b/src/pages/explore/DrugDiseasePairs.jsx index 0eb1336c..7d0f0211 100644 --- a/src/pages/explore/DrugDiseasePairs.jsx +++ b/src/pages/explore/DrugDiseasePairs.jsx @@ -129,12 +129,12 @@ export default function DrugDiseasePairs() { pairs.map((pair, i) => (
-

Disease

+
+

Disease

+ 		-

Drug

+ 		+

Drug

+ 		-

Score

+ 		+

Score
- {pair.disease.name} - {pair.disease.id} + {pair.disease_name} + {pair.disease_id} - {pair.drug.name} - {pair.drug.id} + {pair.drug_name} + {pair.drug_id} {