diff --git a/package-lock.json b/package-lock.json
index 2f9eed3b..42485805 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10,6 +10,7 @@
"license": "MIT",
"dependencies": {
"@auth0/auth0-react": "^1.6.0",
+ "@floating-ui/react": "^0.27.8",
"@material-ui/core": "^4.11.0",
"@material-ui/data-grid": "^4.0.0-alpha.2",
"@material-ui/icons": "^4.9.1",
@@ -17,7 +18,7 @@
"@tanstack/react-table": "^8.20.5",
"ag-grid-community": "^23.2.1",
"ag-grid-react": "^23.2.1",
- "axios": "^0.21.1",
+ "axios": "^0.22.0",
"axios-retry": "^3.1.8",
"body-parser": "^1.20.0",
"bootstrap": "^3.4.1",
@@ -36,10 +37,10 @@
"path": "^0.12.7",
"rc-slider": "^9.3.1",
"rc-tooltip": "^4.2.1",
- "react": "^16.13.1",
+ "react": "^17.0.2",
"react-bootstrap": "^0.33.1",
"react-bootstrap-dialog": "^0.13.0",
- "react-dom": "^16.13.1",
+ "react-dom": "^17.0.2",
"react-dropzone": "^11.0.2",
"react-graph-vis": "^1.0.5",
"react-icons": "^3.10.0",
@@ -53,6 +54,7 @@
"react-virtualized": "^9.21.2",
"react-widgets": "^4.5.0",
"regenerator-runtime": "^0.13.7",
+ "rich-textarea": "^0.26.4",
"shortid": "^2.2.15",
"slugify": "^1.4.5",
"sqlite3": "^5.1.7"
@@ -3848,11 +3850,15 @@
}
},
"node_modules/@babel/runtime": {
- "version": "7.10.5",
- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.10.5.tgz",
- "integrity": "sha512-otddXKhdNn7d0ptoFRHtMLa8LqDxLYwTjB4nYgM1yy5N6gU/MUf8zqyyLltCH3yAVitBzmwK4us+DD0l/MauAg==",
+ "version": "7.27.0",
+ "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.27.0.tgz",
+ "integrity": "sha512-VtPOkrdPHZsKc/clNqyi9WUA8TINkZ4cGk63UUE3u4pmB2k+ZMQRDuIOagv8UVd6j7k0T3+RRIb7beKTebNbcw==",
+ "license": "MIT",
"dependencies": {
- "regenerator-runtime": "^0.13.4"
+ "regenerator-runtime": "^0.14.0"
+ },
+ "engines": {
+ "node": ">=6.9.0"
}
},
"node_modules/@babel/runtime-corejs2": {
@@ -3893,9 +3899,10 @@
"dev": true
},
"node_modules/@babel/runtime/node_modules/regenerator-runtime": {
- "version": "0.13.5",
- "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.13.5.tgz",
- "integrity": "sha512-ZS5w8CpKFinUzOwW3c83oPeVXoNsrLsaCoLtJvAClH135j/R77RuymhiSErhm2lKcwSCIpmvIWSbDkIfAqKQlA=="
+ "version": "0.14.1",
+ "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.14.1.tgz",
+ "integrity": "sha512-dYnhHh0nJoMfnkZs6GmmhFknAGRrLznOu5nc9ML+EJxGvrx6H7teuevqVqCuPcPK//3eDrrjQhehXVx9cnkGdw==",
+ "license": "MIT"
},
"node_modules/@babel/template": {
"version": "7.10.4",
@@ -4053,6 +4060,59 @@
"resolved": "https://registry.npmjs.org/@emotion/weak-memoize/-/weak-memoize-0.2.5.tgz",
"integrity": "sha512-6U71C2Wp7r5XtFtQzYrW5iKFT67OixrSxjI4MptCHzdSVlgabczzqLe0ZSgnub/5Kp4hSbpDB1tMytZY9pwxxA=="
},
+ "node_modules/@floating-ui/core": {
+ "version": "1.6.9",
+ "resolved": "https://registry.npmjs.org/@floating-ui/core/-/core-1.6.9.tgz",
+ "integrity": "sha512-uMXCuQ3BItDUbAMhIXw7UPXRfAlOAvZzdK9BWpE60MCn+Svt3aLn9jsPTi/WNGlRUu2uI0v5S7JiIUsbsvh3fw==",
+ "license": "MIT",
+ "dependencies": {
+ "@floating-ui/utils": "^0.2.9"
+ }
+ },
+ "node_modules/@floating-ui/dom": {
+ "version": "1.6.13",
+ "resolved": "https://registry.npmjs.org/@floating-ui/dom/-/dom-1.6.13.tgz",
+ "integrity": "sha512-umqzocjDgNRGTuO7Q8CU32dkHkECqI8ZdMZ5Swb6QAM0t5rnlrN3lGo1hdpscRd3WS8T6DKYK4ephgIH9iRh3w==",
+ "license": "MIT",
+ "dependencies": {
+ "@floating-ui/core": "^1.6.0",
+ "@floating-ui/utils": "^0.2.9"
+ }
+ },
+ "node_modules/@floating-ui/react": {
+ "version": "0.27.8",
+ "resolved": "https://registry.npmjs.org/@floating-ui/react/-/react-0.27.8.tgz",
+ "integrity": "sha512-EQJ4Th328y2wyHR3KzOUOoTW2UKjFk53fmyahfwExnFQ8vnsMYqKc+fFPOkeYtj5tcp1DUMiNJ7BFhed7e9ONw==",
+ "license": "MIT",
+ "dependencies": {
+ "@floating-ui/react-dom": "^2.1.2",
+ "@floating-ui/utils": "^0.2.9",
+ "tabbable": "^6.0.0"
+ },
+ "peerDependencies": {
+ "react": ">=17.0.0",
+ "react-dom": ">=17.0.0"
+ }
+ },
+ "node_modules/@floating-ui/react-dom": {
+ "version": "2.1.2",
+ "resolved": "https://registry.npmjs.org/@floating-ui/react-dom/-/react-dom-2.1.2.tgz",
+ "integrity": "sha512-06okr5cgPzMNBy+Ycse2A6udMi4bqwW/zgBF/rwjcNqWkyr82Mcg8b0vjX8OJpZFy/FKjJmw6wV7t44kK6kW7A==",
+ "license": "MIT",
+ "dependencies": {
+ "@floating-ui/dom": "^1.0.0"
+ },
+ "peerDependencies": {
+ "react": ">=16.8.0",
+ "react-dom": ">=16.8.0"
+ }
+ },
+ "node_modules/@floating-ui/utils": {
+ "version": "0.2.9",
+ "resolved": "https://registry.npmjs.org/@floating-ui/utils/-/utils-0.2.9.tgz",
+ "integrity": "sha512-MDWhGtE+eHw5JW7lq4qhc5yRLS11ERl1c7Z6Xd0a58DozHES6EnNNwUWbMiG4J9Cgj053Bhk8zvlhFYKVhULwg==",
+ "license": "MIT"
+ },
"node_modules/@gar/promisify": {
"version": "1.1.3",
"resolved": "https://registry.npmjs.org/@gar/promisify/-/promisify-1.1.3.tgz",
@@ -5450,46 +5510,6 @@
}
}
},
- "node_modules/@material-ui/core/node_modules/csstype": {
- "version": "3.0.2",
- "resolved": "https://registry.npmjs.org/csstype/-/csstype-3.0.2.tgz",
- "integrity": "sha512-ofovWglpqoqbfLNOTBNZLSbMuGrblAf1efvvArGKOZMBrIoJeu5UsAipQolkijtyQx5MtAzT/J9IHj/CEY1mJw=="
- },
- "node_modules/@material-ui/core/node_modules/dom-helpers": {
- "version": "5.2.0",
- "resolved": "https://registry.npmjs.org/dom-helpers/-/dom-helpers-5.2.0.tgz",
- "integrity": "sha512-Ru5o9+V8CpunKnz5LGgWXkmrH/20cGKwcHwS4m73zIvs54CN9epEmT/HLqFJW3kXpakAFkEdzgy1hzlJe3E4OQ==",
- "dependencies": {
- "@babel/runtime": "^7.8.7",
- "csstype": "^3.0.2"
- }
- },
- "node_modules/@material-ui/core/node_modules/loose-envify": {
- "version": "1.4.0",
- "resolved": "https://registry.npmjs.org/loose-envify/-/loose-envify-1.4.0.tgz",
- "integrity": "sha512-lyuxPGr/Wfhrlem2CL/UcnUc1zcqKAImBDzukY7Y5F/yQiNdko6+fRLevlw1HgMySw7f611UIY408EtxRSoK3Q==",
- "dependencies": {
- "js-tokens": "^3.0.0 || ^4.0.0"
- },
- "bin": {
- "loose-envify": "cli.js"
- }
- },
- "node_modules/@material-ui/core/node_modules/react-transition-group": {
- "version": "4.4.1",
- "resolved": "https://registry.npmjs.org/react-transition-group/-/react-transition-group-4.4.1.tgz",
- "integrity": "sha512-Djqr7OQ2aPUiYurhPalTrVy9ddmFCCzwhqQmtN+J3+3DzLO209Fdr70QrN8Z3DsglWql6iY1lDWAfpFiBtuKGw==",
- "dependencies": {
- "@babel/runtime": "^7.5.5",
- "dom-helpers": "^5.0.1",
- "loose-envify": "^1.4.0",
- "prop-types": "^15.6.2"
- },
- "peerDependencies": {
- "react": ">=16.6.0",
- "react-dom": ">=16.6.0"
- }
- },
"node_modules/@material-ui/data-grid": {
"version": "4.0.0-alpha.2",
"resolved": "https://registry.npmjs.org/@material-ui/data-grid/-/data-grid-4.0.0-alpha.2.tgz",
@@ -5562,26 +5582,27 @@
}
},
"node_modules/@material-ui/styles": {
- "version": "4.10.0",
- "resolved": "https://registry.npmjs.org/@material-ui/styles/-/styles-4.10.0.tgz",
- "integrity": "sha512-XPwiVTpd3rlnbfrgtEJ1eJJdFCXZkHxy8TrdieaTvwxNYj42VnnCyFzxYeNW9Lhj4V1oD8YtQ6S5Gie7bZDf7Q==",
+ "version": "4.11.5",
+ "resolved": "https://registry.npmjs.org/@material-ui/styles/-/styles-4.11.5.tgz",
+ "integrity": "sha512-o/41ot5JJiUsIETME9wVLAJrmIWL3j0R0Bj2kCOLbSfqEkKf0fmaPt+5vtblUh5eXr2S+J/8J3DaCb10+CzPGA==",
"deprecated": "Material UI v4 doesn't receive active development since September 2021. See the guide https://mui.com/material-ui/migration/migration-v4/ to upgrade to v5.",
+ "license": "MIT",
"dependencies": {
"@babel/runtime": "^7.4.4",
"@emotion/hash": "^0.8.0",
- "@material-ui/types": "^5.1.0",
- "@material-ui/utils": "^4.9.6",
+ "@material-ui/types": "5.1.0",
+ "@material-ui/utils": "^4.11.3",
"clsx": "^1.0.4",
"csstype": "^2.5.2",
"hoist-non-react-statics": "^3.3.2",
- "jss": "^10.0.3",
- "jss-plugin-camel-case": "^10.0.3",
- "jss-plugin-default-unit": "^10.0.3",
- "jss-plugin-global": "^10.0.3",
- "jss-plugin-nested": "^10.0.3",
- "jss-plugin-props-sort": "^10.0.3",
- "jss-plugin-rule-value-function": "^10.0.3",
- "jss-plugin-vendor-prefixer": "^10.0.3",
+ "jss": "^10.5.1",
+ "jss-plugin-camel-case": "^10.5.1",
+ "jss-plugin-default-unit": "^10.5.1",
+ "jss-plugin-global": "^10.5.1",
+ "jss-plugin-nested": "^10.5.1",
+ "jss-plugin-props-sort": "^10.5.1",
+ "jss-plugin-rule-value-function": "^10.5.1",
+ "jss-plugin-vendor-prefixer": "^10.5.1",
"prop-types": "^15.7.2"
},
"engines": {
@@ -5592,9 +5613,9 @@
"url": "https://opencollective.com/material-ui"
},
"peerDependencies": {
- "@types/react": "^16.8.6",
- "react": "^16.8.0",
- "react-dom": "^16.8.0"
+ "@types/react": "^16.8.6 || ^17.0.0",
+ "react": "^16.8.0 || ^17.0.0",
+ "react-dom": "^16.8.0 || ^17.0.0"
},
"peerDependenciesMeta": {
"@types/react": {
@@ -5603,13 +5624,13 @@
}
},
"node_modules/@material-ui/system": {
- "version": "4.9.14",
- "resolved": "https://registry.npmjs.org/@material-ui/system/-/system-4.9.14.tgz",
- "integrity": "sha512-oQbaqfSnNlEkXEziDcJDDIy8pbvwUmZXWNqlmIwDqr/ZdCK8FuV3f4nxikUh7hvClKV2gnQ9djh5CZFTHkZj3w==",
- "deprecated": "You can now upgrade to @mui/system. See the guide: https://mui.com/guides/migration-v4/",
+ "version": "4.12.2",
+ "resolved": "https://registry.npmjs.org/@material-ui/system/-/system-4.12.2.tgz",
+ "integrity": "sha512-6CSKu2MtmiJgcCGf6nBQpM8fLkuB9F55EKfbdTC80NND5wpTmKzwdhLYLH3zL4cLlK0gVaaltW7/wMuyTnN0Lw==",
+ "license": "MIT",
"dependencies": {
"@babel/runtime": "^7.4.4",
- "@material-ui/utils": "^4.9.6",
+ "@material-ui/utils": "^4.11.3",
"csstype": "^2.5.2",
"prop-types": "^15.7.2"
},
@@ -5621,9 +5642,9 @@
"url": "https://opencollective.com/material-ui"
},
"peerDependencies": {
- "@types/react": "^16.8.6",
- "react": "^16.8.0",
- "react-dom": "^16.8.0"
+ "@types/react": "^16.8.6 || ^17.0.0",
+ "react": "^16.8.0 || ^17.0.0",
+ "react-dom": "^16.8.0 || ^17.0.0"
},
"peerDependenciesMeta": {
"@types/react": {
@@ -5645,20 +5666,21 @@
}
},
"node_modules/@material-ui/utils": {
- "version": "4.10.2",
- "resolved": "https://registry.npmjs.org/@material-ui/utils/-/utils-4.10.2.tgz",
- "integrity": "sha512-eg29v74P7W5r6a4tWWDAAfZldXIzfyO1am2fIsC39hdUUHm/33k6pGOKPbgDjg/U/4ifmgAePy/1OjkKN6rFRw==",
+ "version": "4.11.3",
+ "resolved": "https://registry.npmjs.org/@material-ui/utils/-/utils-4.11.3.tgz",
+ "integrity": "sha512-ZuQPV4rBK/V1j2dIkSSEcH5uT6AaHuKWFfotADHsC0wVL1NLd2WkFCm4ZZbX33iO4ydl6V0GPngKm8HZQ2oujg==",
+ "license": "MIT",
"dependencies": {
"@babel/runtime": "^7.4.4",
"prop-types": "^15.7.2",
- "react-is": "^16.8.0"
+ "react-is": "^16.8.0 || ^17.0.0"
},
"engines": {
"node": ">=8.0.0"
},
"peerDependencies": {
- "react": "^16.8.0",
- "react-dom": "^16.8.0"
+ "react": "^16.8.0 || ^17.0.0",
+ "react-dom": "^16.8.0 || ^17.0.0"
}
},
"node_modules/@mswjs/cookies": {
@@ -6183,36 +6205,6 @@
"react-test-renderer": ">=16.9.0"
}
},
- "node_modules/@testing-library/react-hooks/node_modules/@babel/runtime": {
- "version": "7.12.5",
- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.12.5.tgz",
- "integrity": "sha512-plcc+hbExy3McchJCEQG3knOsuh3HH+Prx1P6cLIkET/0dLuQDEnrT+s27Axgc9bqfsmNUNHfscgMUdBpC9xfg==",
- "dev": true,
- "dependencies": {
- "regenerator-runtime": "^0.13.4"
- }
- },
- "node_modules/@testing-library/react-hooks/node_modules/regenerator-runtime": {
- "version": "0.13.7",
- "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.13.7.tgz",
- "integrity": "sha512-a54FxoJDIr27pgf7IgeQGxmqUNYrcV338lf/6gH456HZ/PhX+5BcwHXG9ajESmwe6WRO0tAzRUrRmNONWgkrew==",
- "dev": true
- },
- "node_modules/@testing-library/react/node_modules/@babel/runtime": {
- "version": "7.12.5",
- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.12.5.tgz",
- "integrity": "sha512-plcc+hbExy3McchJCEQG3knOsuh3HH+Prx1P6cLIkET/0dLuQDEnrT+s27Axgc9bqfsmNUNHfscgMUdBpC9xfg==",
- "dev": true,
- "dependencies": {
- "regenerator-runtime": "^0.13.4"
- }
- },
- "node_modules/@testing-library/react/node_modules/regenerator-runtime": {
- "version": "0.13.7",
- "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.13.7.tgz",
- "integrity": "sha512-a54FxoJDIr27pgf7IgeQGxmqUNYrcV338lf/6gH456HZ/PhX+5BcwHXG9ajESmwe6WRO0tAzRUrRmNONWgkrew==",
- "dev": true
- },
"node_modules/@testing-library/user-event": {
"version": "13.2.1",
"resolved": "https://registry.npmjs.org/@testing-library/user-event/-/user-event-13.2.1.tgz",
@@ -6229,18 +6221,6 @@
"@testing-library/dom": ">=7.21.4"
}
},
- "node_modules/@testing-library/user-event/node_modules/@babel/runtime": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.15.4.tgz",
- "integrity": "sha512-99catp6bHCaxr4sJ/DbTGgHS4+Rs2RVd2g7iOap6SLGPDknRK9ztKNsE/Fg6QhSeh1FGE5f6gHGQmvvn3I3xhw==",
- "dev": true,
- "dependencies": {
- "regenerator-runtime": "^0.13.4"
- },
- "engines": {
- "node": ">=6.9.0"
- }
- },
"node_modules/@tootallnate/once": {
"version": "1.1.2",
"resolved": "https://registry.npmjs.org/@tootallnate/once/-/once-1.1.2.tgz",
@@ -7906,11 +7886,12 @@
}
},
"node_modules/axios": {
- "version": "0.21.1",
- "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.1.tgz",
- "integrity": "sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==",
+ "version": "0.22.0",
+ "resolved": "https://registry.npmjs.org/axios/-/axios-0.22.0.tgz",
+ "integrity": "sha512-Z0U3uhqQeg1oNcihswf4ZD57O3NrR1+ZXhxaROaWpDmsDTx7T2HNBV2ulBtie2hwJptu8UvgnJoK+BIqdzh/1w==",
+ "license": "MIT",
"dependencies": {
- "follow-redirects": "^1.10.0"
+ "follow-redirects": "^1.14.4"
}
},
"node_modules/axios-retry": {
@@ -7921,25 +7902,6 @@
"is-retry-allowed": "^1.1.0"
}
},
- "node_modules/axios/node_modules/follow-redirects": {
- "version": "1.13.2",
- "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.13.2.tgz",
- "integrity": "sha512-6mPTgLxYm3r6Bkkg0vNM0HTjfGrOEtsfbhagQvbxDEsEkpNhw582upBaoRZylzen6krEmxXJgt9Ju6HiI4O7BA==",
- "funding": [
- {
- "type": "individual",
- "url": "https://github.com/sponsors/RubenVerborgh"
- }
- ],
- "engines": {
- "node": ">=4.0"
- },
- "peerDependenciesMeta": {
- "debug": {
- "optional": true
- }
- }
- },
"node_modules/axobject-query": {
"version": "2.2.0",
"resolved": "https://registry.npmjs.org/axobject-query/-/axobject-query-2.2.0.tgz",
@@ -10246,6 +10208,7 @@
"version": "2.0.8",
"resolved": "https://registry.npmjs.org/css-vendor/-/css-vendor-2.0.8.tgz",
"integrity": "sha512-x9Aq0XTInxrkuFeHKbYC7zWY8ai7qJ04Kxd9MnvbC1uO5DagxoHQjm4JvG+vCdXOoFtCjbL2XSZfxmoYa9uQVQ==",
+ "license": "MIT",
"dependencies": {
"@babel/runtime": "^7.8.3",
"is-in-browser": "^1.0.2"
@@ -11081,9 +11044,10 @@
"dev": true
},
"node_modules/dom-align": {
- "version": "1.12.0",
- "resolved": "https://registry.npmjs.org/dom-align/-/dom-align-1.12.0.tgz",
- "integrity": "sha512-YkoezQuhp3SLFGdOlr5xkqZ640iXrnHAwVYcDg8ZKRUtO7mSzSC2BA5V0VuyAwPSJA4CLIc6EDDJh4bEsD2+zA=="
+ "version": "1.12.4",
+ "resolved": "https://registry.npmjs.org/dom-align/-/dom-align-1.12.4.tgz",
+ "integrity": "sha512-R8LUSEay/68zE5c8/3BDxiTEvgb4xZTF0RKmAHfiEVN3klfIpXfi2/QCoiWPccVQ0J/ZGdz9OjzL4uJEP/MRAw==",
+ "license": "MIT"
},
"node_modules/dom-converter": {
"version": "0.2.0",
@@ -12137,18 +12101,6 @@
"node": ">=10"
}
},
- "node_modules/eslint-plugin-jest-dom/node_modules/@testing-library/dom/node_modules/@babel/runtime": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.15.4.tgz",
- "integrity": "sha512-99catp6bHCaxr4sJ/DbTGgHS4+Rs2RVd2g7iOap6SLGPDknRK9ztKNsE/Fg6QhSeh1FGE5f6gHGQmvvn3I3xhw==",
- "dev": true,
- "dependencies": {
- "regenerator-runtime": "^0.13.4"
- },
- "engines": {
- "node": ">=6.9.0"
- }
- },
"node_modules/eslint-plugin-jest-dom/node_modules/ansi-styles": {
"version": "4.3.0",
"resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
@@ -13663,24 +13615,23 @@
}
},
"node_modules/follow-redirects": {
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"deprecated": "Package no longer supported. Contact Support at https://www.npmjs.com/support for more info.",
+ "license": "MIT",
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+ "@babel/runtime": "^7.12.1",
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},
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- "react-dom": "*"
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@@ -25537,6 +25498,22 @@
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+ "license": "MIT",
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@@ -25565,17 +25543,27 @@
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+ "license": "MIT",
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+ "dependencies": {
+ "loose-envify": "^1.1.0",
+ "object-assign": "^4.1.1"
}
},
"node_modules/react-dropzone": {
@@ -25626,17 +25614,6 @@
"react": "*"
}
},
- "node_modules/react-input-autosize": {
- "version": "2.2.2",
- "resolved": "https://registry.npmjs.org/react-input-autosize/-/react-input-autosize-2.2.2.tgz",
- "integrity": "sha512-jQJgYCA3S0j+cuOwzuCd1OjmBmnZLdqQdiLKRYrsMMzbjUrVDS5RvJUDwJqA7sKuksDuzFtm6hZGKFu7Mjk5aw==",
- "dependencies": {
- "prop-types": "^15.5.8"
- },
- "peerDependencies": {
- "react": "^0.14.9 || ^15.3.0 || ^16.0.0-rc || ^16.0"
- }
- },
"node_modules/react-is": {
"version": "16.13.1",
"resolved": "https://registry.npmjs.org/react-is/-/react-is-16.13.1.tgz",
@@ -25657,6 +25634,18 @@
"react-dom": "^17.0.0 || ^16.3.0 || ^15.5.4"
}
},
+ "node_modules/react-json-view/node_modules/react-textarea-autosize": {
+ "version": "6.1.0",
+ "resolved": "https://registry.npmjs.org/react-textarea-autosize/-/react-textarea-autosize-6.1.0.tgz",
+ "integrity": "sha512-F6bI1dgib6fSvG8so1HuArPUv+iVEfPliuLWusLF+gAKz0FbB4jLrWUrTAeq1afnPT2c9toEZYUdz/y1uKMy4A==",
+ "license": "MIT",
+ "dependencies": {
+ "prop-types": "^15.6.0"
+ },
+ "peerDependencies": {
+ "react": ">=0.14.0 <17.0.0"
+ }
+ },
"node_modules/react-lifecycles-compat": {
"version": "3.0.4",
"resolved": "https://registry.npmjs.org/react-lifecycles-compat/-/react-lifecycles-compat-3.0.4.tgz",
@@ -25676,9 +25665,10 @@
}
},
"node_modules/react-overlays": {
- "version": "0.9.1",
- "resolved": "https://registry.npmjs.org/react-overlays/-/react-overlays-0.9.1.tgz",
- "integrity": "sha512-b0asy/zHtRd0i2+2/uNxe3YVprF3bRT1guyr791DORjCzE/HSBMog+ul83CdtKQ1kZ+pLnxWCu5W3BMysFhHdQ==",
+ "version": "0.9.3",
+ "resolved": "https://registry.npmjs.org/react-overlays/-/react-overlays-0.9.3.tgz",
+ "integrity": "sha512-u2T7nOLnK+Hrntho4p0Nxh+BsJl0bl4Xuwj/Y0a56xywLMetgAfyjnDVrudLXsNcKGaspoC+t3C1V80W9QQTdQ==",
+ "license": "MIT",
"dependencies": {
"classnames": "^2.2.5",
"dom-helpers": "^3.2.1",
@@ -25692,6 +25682,22 @@
"react-dom": ">=16.3.0"
}
},
+ "node_modules/react-overlays/node_modules/react-transition-group": {
+ "version": "2.9.0",
+ "resolved": "https://registry.npmjs.org/react-transition-group/-/react-transition-group-2.9.0.tgz",
+ "integrity": "sha512-+HzNTCHpeQyl4MJ/bdE0u6XRMe9+XG/+aL4mCxVN4DnPBQ0/5bfHWPDuOZUzYdMj94daZaZdCCc1Dzt9R/xSSg==",
+ "license": "BSD-3-Clause",
+ "dependencies": {
+ "dom-helpers": "^3.4.0",
+ "loose-envify": "^1.4.0",
+ "prop-types": "^15.6.2",
+ "react-lifecycles-compat": "^3.0.4"
+ },
+ "peerDependencies": {
+ "react": ">=15.0.0",
+ "react-dom": ">=15.0.0"
+ }
+ },
"node_modules/react-prop-types": {
"version": "0.4.0",
"resolved": "https://registry.npmjs.org/react-prop-types/-/react-prop-types-0.4.0.tgz",
@@ -25781,39 +25787,16 @@
"react-dom": "^16.8.0"
}
},
- "node_modules/react-select/node_modules/dom-helpers": {
- "version": "5.1.4",
- "resolved": "https://registry.npmjs.org/dom-helpers/-/dom-helpers-5.1.4.tgz",
- "integrity": "sha512-TjMyeVUvNEnOnhzs6uAn9Ya47GmMo3qq7m+Lr/3ON0Rs5kHvb8I+SQYjLUSYn7qhEm0QjW0yrBkvz9yOrwwz1A==",
- "dependencies": {
- "@babel/runtime": "^7.8.7",
- "csstype": "^2.6.7"
- }
- },
- "node_modules/react-select/node_modules/loose-envify": {
- "version": "1.4.0",
- "resolved": "https://registry.npmjs.org/loose-envify/-/loose-envify-1.4.0.tgz",
- "integrity": "sha512-lyuxPGr/Wfhrlem2CL/UcnUc1zcqKAImBDzukY7Y5F/yQiNdko6+fRLevlw1HgMySw7f611UIY408EtxRSoK3Q==",
- "dependencies": {
- "js-tokens": "^3.0.0 || ^4.0.0"
- },
- "bin": {
- "loose-envify": "cli.js"
- }
- },
- "node_modules/react-select/node_modules/react-transition-group": {
- "version": "4.4.1",
- "resolved": "https://registry.npmjs.org/react-transition-group/-/react-transition-group-4.4.1.tgz",
- "integrity": "sha512-Djqr7OQ2aPUiYurhPalTrVy9ddmFCCzwhqQmtN+J3+3DzLO209Fdr70QrN8Z3DsglWql6iY1lDWAfpFiBtuKGw==",
+ "node_modules/react-select/node_modules/react-input-autosize": {
+ "version": "2.2.2",
+ "resolved": "https://registry.npmjs.org/react-input-autosize/-/react-input-autosize-2.2.2.tgz",
+ "integrity": "sha512-jQJgYCA3S0j+cuOwzuCd1OjmBmnZLdqQdiLKRYrsMMzbjUrVDS5RvJUDwJqA7sKuksDuzFtm6hZGKFu7Mjk5aw==",
+ "license": "MIT",
"dependencies": {
- "@babel/runtime": "^7.5.5",
- "dom-helpers": "^5.0.1",
- "loose-envify": "^1.4.0",
- "prop-types": "^15.6.2"
+ "prop-types": "^15.5.8"
},
"peerDependencies": {
- "react": ">=16.6.0",
- "react-dom": ">=16.6.0"
+ "react": "^0.14.9 || ^15.3.0 || ^16.0.0-rc || ^16.0"
}
},
"node_modules/react-split-pane": {
@@ -25878,41 +25861,36 @@
"react": "^16.13.1"
}
},
- "node_modules/react-textarea-autosize": {
- "version": "6.1.0",
- "resolved": "https://registry.npmjs.org/react-textarea-autosize/-/react-textarea-autosize-6.1.0.tgz",
- "integrity": "sha512-F6bI1dgib6fSvG8so1HuArPUv+iVEfPliuLWusLF+gAKz0FbB4jLrWUrTAeq1afnPT2c9toEZYUdz/y1uKMy4A==",
- "dependencies": {
- "prop-types": "^15.6.0"
- },
- "peerDependencies": {
- "react": ">=0.14.0 <17.0.0"
- }
- },
"node_modules/react-transition-group": {
- "version": "2.9.0",
- "resolved": "https://registry.npmjs.org/react-transition-group/-/react-transition-group-2.9.0.tgz",
- "integrity": "sha512-+HzNTCHpeQyl4MJ/bdE0u6XRMe9+XG/+aL4mCxVN4DnPBQ0/5bfHWPDuOZUzYdMj94daZaZdCCc1Dzt9R/xSSg==",
+ "version": "4.4.5",
+ "resolved": "https://registry.npmjs.org/react-transition-group/-/react-transition-group-4.4.5.tgz",
+ "integrity": "sha512-pZcd1MCJoiKiBR2NRxeCRg13uCXbydPnmB4EOeRrY7480qNWO8IIgQG6zlDkm6uRMsURXPuKq0GWtiM59a5Q6g==",
+ "license": "BSD-3-Clause",
"dependencies": {
- "dom-helpers": "^3.4.0",
+ "@babel/runtime": "^7.5.5",
+ "dom-helpers": "^5.0.1",
"loose-envify": "^1.4.0",
- "prop-types": "^15.6.2",
- "react-lifecycles-compat": "^3.0.4"
+ "prop-types": "^15.6.2"
},
"peerDependencies": {
- "react": ">=15.0.0",
- "react-dom": ">=15.0.0"
+ "react": ">=16.6.0",
+ "react-dom": ">=16.6.0"
}
},
- "node_modules/react-transition-group/node_modules/loose-envify": {
- "version": "1.4.0",
- "resolved": "https://registry.npmjs.org/loose-envify/-/loose-envify-1.4.0.tgz",
- "integrity": "sha512-lyuxPGr/Wfhrlem2CL/UcnUc1zcqKAImBDzukY7Y5F/yQiNdko6+fRLevlw1HgMySw7f611UIY408EtxRSoK3Q==",
+ "node_modules/react-transition-group/node_modules/csstype": {
+ "version": "3.1.3",
+ "resolved": "https://registry.npmjs.org/csstype/-/csstype-3.1.3.tgz",
+ "integrity": "sha512-M1uQkMl8rQK/szD0LNhtqxIPLpimGm8sOBwU7lLnCpSbTyY3yeU1Vc7l4KT5zT4s/yOxHH5O7tIuuLOCnLADRw==",
+ "license": "MIT"
+ },
+ "node_modules/react-transition-group/node_modules/dom-helpers": {
+ "version": "5.2.1",
+ "resolved": "https://registry.npmjs.org/dom-helpers/-/dom-helpers-5.2.1.tgz",
+ "integrity": "sha512-nRCa7CK3VTrM2NmGkIy4cbK7IZlgBE/PYMn55rrXefr5xXDP0LdtfPnblFDoVdcAfslJ7or6iqAUnx0CCGIWQA==",
+ "license": "MIT",
"dependencies": {
- "js-tokens": "^3.0.0 || ^4.0.0"
- },
- "bin": {
- "loose-envify": "cli.js"
+ "@babel/runtime": "^7.8.7",
+ "csstype": "^3.0.2"
}
},
"node_modules/react-virtualized": {
@@ -25962,6 +25940,22 @@
"react-dom": ">=0.14.0"
}
},
+ "node_modules/react-widgets/node_modules/react-transition-group": {
+ "version": "2.9.0",
+ "resolved": "https://registry.npmjs.org/react-transition-group/-/react-transition-group-2.9.0.tgz",
+ "integrity": "sha512-+HzNTCHpeQyl4MJ/bdE0u6XRMe9+XG/+aL4mCxVN4DnPBQ0/5bfHWPDuOZUzYdMj94daZaZdCCc1Dzt9R/xSSg==",
+ "license": "BSD-3-Clause",
+ "dependencies": {
+ "dom-helpers": "^3.4.0",
+ "loose-envify": "^1.4.0",
+ "prop-types": "^15.6.2",
+ "react-lifecycles-compat": "^3.0.4"
+ },
+ "peerDependencies": {
+ "react": ">=15.0.0",
+ "react-dom": ">=15.0.0"
+ }
+ },
"node_modules/read-pkg": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/read-pkg/-/read-pkg-2.0.0.tgz",
@@ -26315,7 +26309,8 @@
"node_modules/resize-observer-polyfill": {
"version": "1.5.1",
"resolved": "https://registry.npmjs.org/resize-observer-polyfill/-/resize-observer-polyfill-1.5.1.tgz",
- "integrity": "sha512-LwZrotdHOo12nQuZlHEmtuXdqGoOD0OhaxopaNFxWzInpEgaLWoVuAMbTzixuosCx2nEG58ngzW3vxdWoxIgdg=="
+ "integrity": "sha512-LwZrotdHOo12nQuZlHEmtuXdqGoOD0OhaxopaNFxWzInpEgaLWoVuAMbTzixuosCx2nEG58ngzW3vxdWoxIgdg==",
+ "license": "MIT"
},
"node_modules/resolve": {
"version": "1.7.0",
@@ -26435,6 +26430,15 @@
"node": ">=0.10.0"
}
},
+ "node_modules/rich-textarea": {
+ "version": "0.26.4",
+ "resolved": "https://registry.npmjs.org/rich-textarea/-/rich-textarea-0.26.4.tgz",
+ "integrity": "sha512-RMEEUg3eNkHQc8+Joq+W+70KS5dZGXpWaIU5qiIouNAGBhVOX1vC1TpPUeysfLmqlqQOuqP81rWpgaXldkJP7A==",
+ "license": "MIT",
+ "peerDependencies": {
+ "react": ">=16.14.0"
+ }
+ },
"node_modules/rimraf": {
"version": "2.7.1",
"resolved": "https://registry.npmjs.org/rimraf/-/rimraf-2.7.1.tgz",
@@ -26550,6 +26554,7 @@
"version": "0.19.1",
"resolved": "https://registry.npmjs.org/scheduler/-/scheduler-0.19.1.tgz",
"integrity": "sha512-n/zwRWRYSUj0/3g/otKDRPMh6qv2SYMWNq85IEa8iZyAv8od9zDYpGSnpBEjNgcMNq6Scbu5KfIPxNF72R/2EA==",
+ "dev": true,
"dependencies": {
"loose-envify": "^1.1.0",
"object-assign": "^4.1.1"
@@ -27455,7 +27460,8 @@
"node_modules/spy-on-component": {
"version": "1.1.3",
"resolved": "https://registry.npmjs.org/spy-on-component/-/spy-on-component-1.1.3.tgz",
- "integrity": "sha512-a7jgnoBSdkcDWIQQwtEgUq4etajwG6+wGIjfC9ARUKwKOdHxJd+utgHTgLn81ETizpsw4xddUS3W8VePedtaIQ=="
+ "integrity": "sha512-a7jgnoBSdkcDWIQQwtEgUq4etajwG6+wGIjfC9ARUKwKOdHxJd+utgHTgLn81ETizpsw4xddUS3W8VePedtaIQ==",
+ "license": "MIT"
},
"node_modules/sqlite3": {
"version": "5.1.7",
@@ -27949,6 +27955,12 @@
"integrity": "sha512-9QNk5KwDF+Bvz+PyObkmSYjI5ksVUYtjW7AU22r2NKcfLJcXp96hkDWU3+XndOsUb+AQ9QhfzfCT2O+CNWT5Tw==",
"dev": true
},
+ "node_modules/tabbable": {
+ "version": "6.2.0",
+ "resolved": "https://registry.npmjs.org/tabbable/-/tabbable-6.2.0.tgz",
+ "integrity": "sha512-Cat63mxsVJlzYvN51JmVXIgNoUokrIaT2zLclCXjRd8boZ0004U4KCs/sToJ75C6sdlByWxpYnb5Boif1VSFew==",
+ "license": "MIT"
+ },
"node_modules/table": {
"version": "5.4.6",
"resolved": "https://registry.npmjs.org/table/-/table-5.4.6.tgz",
@@ -28511,21 +28523,6 @@
"is-typedarray": "^1.0.0"
}
},
- "node_modules/typescript": {
- "version": "5.6.3",
- "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.6.3.tgz",
- "integrity": "sha512-hjcS1mhfuyi4WW8IWtjP7brDrG2cuDZukyrYrSauoXGNgx0S7zceP07adYkJycEr56BOUTNPzbInooiN3fn1qw==",
- "dev": true,
- "license": "Apache-2.0",
- "peer": true,
- "bin": {
- "tsc": "bin/tsc",
- "tsserver": "bin/tsserver"
- },
- "engines": {
- "node": ">=14.17"
- }
- },
"node_modules/ua-parser-js": {
"version": "0.7.28",
"resolved": "https://registry.npmjs.org/ua-parser-js/-/ua-parser-js-0.7.28.tgz",
@@ -28994,16 +28991,6 @@
"node": ">= 0.4.0"
}
},
- "node_modules/uuid": {
- "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",
"resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.1.1.tgz",
@@ -29122,20 +29109,6 @@
"url": "https://opencollective.com/visjs"
}
},
- "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": ">=8"
- },
- "funding": {
- "type": "opencollective",
- "url": "https://opencollective.com/visjs"
- }
- },
"node_modules/vis-uuid": {
"version": "1.1.3",
"resolved": "https://registry.npmjs.org/vis-uuid/-/vis-uuid-1.1.3.tgz",
diff --git a/package.json b/package.json
index 8988f48d..1773de23 100644
--- a/package.json
+++ b/package.json
@@ -46,6 +46,7 @@
},
"dependencies": {
"@auth0/auth0-react": "^1.6.0",
+ "@floating-ui/react": "^0.27.8",
"@material-ui/core": "^4.11.0",
"@material-ui/data-grid": "^4.0.0-alpha.2",
"@material-ui/icons": "^4.9.1",
@@ -53,7 +54,7 @@
"@tanstack/react-table": "^8.20.5",
"ag-grid-community": "^23.2.1",
"ag-grid-react": "^23.2.1",
- "axios": "^0.21.1",
+ "axios": "^0.22.0",
"axios-retry": "^3.1.8",
"body-parser": "^1.20.0",
"bootstrap": "^3.4.1",
@@ -72,10 +73,10 @@
"path": "^0.12.7",
"rc-slider": "^9.3.1",
"rc-tooltip": "^4.2.1",
- "react": "^16.13.1",
+ "react": "^17.0.2",
"react-bootstrap": "^0.33.1",
"react-bootstrap-dialog": "^0.13.0",
- "react-dom": "^16.13.1",
+ "react-dom": "^17.0.2",
"react-dropzone": "^11.0.2",
"react-graph-vis": "^1.0.5",
"react-icons": "^3.10.0",
@@ -89,6 +90,7 @@
"react-virtualized": "^9.21.2",
"react-widgets": "^4.5.0",
"regenerator-runtime": "^0.13.7",
+ "rich-textarea": "^0.26.4",
"shortid": "^2.2.15",
"slugify": "^1.4.5",
"sqlite3": "^5.1.7"
diff --git a/src/hooks/use-query.js b/src/hooks/use-query.js
new file mode 100644
index 00000000..11fa2fc5
--- /dev/null
+++ b/src/hooks/use-query.js
@@ -0,0 +1,144 @@
+import React, {
+ createContext, useCallback, useContext, useEffect, useRef, useState,
+} from 'react';
+
+const CACHE_TTL_MS = 30 * 60 * 1000;
+const PRUNE_INTERVAL_MS = 5 * 60 * 1000;
+
+const QueryCacheContext = createContext(null);
+
+export const QueryCacheProvider = ({ children }) => {
+ const [cache, setCache] = useState(new Map());
+
+ const get = useCallback((key) => {
+ const entry = cache.get(key);
+ if (!entry) return undefined;
+
+ const now = Date.now();
+ if (now - entry.timestamp > CACHE_TTL_MS) {
+ setCache((prev) => {
+ const next = new Map(prev);
+ next.delete(key);
+ return next;
+ });
+ return undefined;
+ }
+
+ return entry.data;
+ }, [cache]);
+
+ const set = useCallback((key, value) => {
+ setCache((prev) => {
+ const next = new Map(prev);
+ next.set(key, { data: value, timestamp: Date.now() });
+ return next;
+ });
+ }, []);
+
+ useEffect(() => {
+ const interval = setInterval(() => {
+ setCache((prev) => {
+ const now = Date.now();
+ const next = new Map(prev);
+ // eslint-disable-next-line no-restricted-syntax
+ for (const [key, entry] of next.entries()) {
+ if (now - entry.timestamp > CACHE_TTL_MS) {
+ next.delete(key);
+ }
+ }
+ return next;
+ });
+ }, PRUNE_INTERVAL_MS);
+
+ return () => clearInterval(interval);
+ }, []);
+
+ return (
+
+ {children}
+
+ );
+};
+
+export const useQuery = ({
+ queryFn,
+ queryKey,
+ debounceMs = 0,
+ keepStaleData = false,
+}) => {
+ const [data, setData] = useState(null);
+ const [isLoading, setIsLoading] = useState(true);
+ const [error, setError] = useState(null);
+
+ const cache = useContext(QueryCacheContext);
+ if (!cache) throw new Error('You must use `useQuery` hook within `QueryCacheProvider`');
+
+ const timeoutRef = useRef(null);
+ const abortControllerRef = useRef(null);
+
+ useEffect(() => {
+ let ignore = false;
+
+ if (timeoutRef.current) {
+ clearTimeout(timeoutRef.current);
+ }
+
+ if (abortControllerRef.current) {
+ abortControllerRef.current.abort();
+ }
+
+ timeoutRef.current = setTimeout(() => {
+ (async () => {
+ if (!keepStaleData) setData(null);
+ setIsLoading(true);
+ setError(null);
+
+ const cachedData = cache.get(queryKey);
+ if (cachedData) {
+ setData(cachedData);
+ setIsLoading(false);
+ return;
+ }
+
+ const controller = new AbortController();
+ abortControllerRef.current = controller;
+
+ try {
+ const d = await queryFn(controller.signal);
+
+ if (ignore) return;
+
+ cache.set(queryKey, d);
+ setData(d);
+ setIsLoading(false);
+ } catch (err) {
+ if (!controller.signal.aborted) {
+ setError((Boolean(err) && err.message) || 'Unknown error');
+ setIsLoading(false);
+ }
+ }
+ })();
+ }, debounceMs);
+
+ return () => {
+ ignore = true;
+ if (timeoutRef.current) {
+ clearTimeout(timeoutRef.current);
+ }
+ if (abortControllerRef.current) {
+ abortControllerRef.current.abort();
+ }
+ };
+
+ // Don't rerender if queryFn is different, this can cause an endless render loop if
+ // the component calling useQuery uses a closure like queryFn: () => fetchFn(someLocalVar).
+
+ // This could be fixed by wrapping the closure in a useCallback in the calling component
+ // or including a dependency array in this hook. All should work fine if all the queryFn
+ // depends on is included in the queryKey.
+
+ // eslint-disable-next-line react-hooks/exhaustive-deps
+ }, [queryKey, cache, debounceMs]);
+
+ return { data, isLoading, error };
+};
diff --git a/src/pages/EnrichedQueries/EnrichedQueries.jsx b/src/pages/EnrichedQueries/EnrichedQueries.jsx
new file mode 100644
index 00000000..85b12ee3
--- /dev/null
+++ b/src/pages/EnrichedQueries/EnrichedQueries.jsx
@@ -0,0 +1,269 @@
+/* eslint-disable no-restricted-syntax */
+import React, { useContext, useRef, useState } from 'react';
+import { Col, Grid, Row } from 'react-bootstrap';
+import { Link } from 'react-router-dom';
+import { Button } from '@material-ui/core';
+import axios from 'axios';
+import csv from 'csv-stringify';
+import Select from './Select';
+import { QueryCacheProvider } from '../../hooks/use-query';
+import NodeInputBox from './NodeInputBox';
+import BiolinkContext from '~/context/biolink';
+
+function generateEnrichmentQuery(inputNodeType, outputNodeType, inputCuries, predicate, inputIsSubject = false) {
+ return {
+ message: {
+ query_graph: {
+ nodes: {
+ input: {
+ categories: [inputNodeType],
+ ids: ['uuid:1'],
+ member_ids: inputCuries,
+ set_interpretation: 'MANY',
+ },
+ output: {
+ categories: [outputNodeType],
+ },
+ },
+ edges: {
+ edge_0: {
+ subject: inputIsSubject ? 'input' : 'output',
+ object: inputIsSubject ? 'output' : 'input',
+ predicates: [predicate],
+ // knowledge_type: "inferred"
+ },
+ },
+ },
+ },
+ };
+}
+
+function extractResultsStructured(resp) {
+ const resultsArray = [];
+
+ const results = resp.message.results || [];
+ const kgNodes = resp.message.knowledge_graph.nodes || {};
+ const kgEdges = resp.message.knowledge_graph.edges || {};
+
+ for (const result of results) {
+ const nb = result.node_bindings.output[0].id;
+ const name = (Boolean(kgNodes[nb]) && kgNodes[nb].name) || 'N/A';
+
+ const edgeId = result.analyses[0].edge_bindings.edge_0[0].id;
+ const edge = kgEdges[edgeId];
+ let pValue = null;
+
+ for (const att of edge.attributes || []) {
+ if (att.attribute_type_id === 'biolink:p_value') {
+ pValue = att.value;
+ break;
+ }
+ }
+
+ resultsArray.push({
+ id: nb,
+ name,
+ p_value: pValue,
+ });
+ }
+
+ return resultsArray;
+}
+
+export default function EnrichedQueries() {
+ const { concepts: categories, predicates } = useContext(BiolinkContext);
+
+ const [curies, setCuries] = useState([]);
+ const [inputNodeType, setInputNodeType] = useState(undefined);
+ const [inputNodeTaxa, setInputNodeTaxa] = useState('');
+ const [relationship, setRelationship] = useState('related_to');
+ const [outputType, setOutputType] = useState('NamedThing');
+
+ const abortControllerRef = useRef(null);
+ const [isLoading, setIsLoading] = useState(false);
+ const [results, setResults] = useState([]);
+
+ function stopQuery() {
+ if (abortControllerRef.current) {
+ abortControllerRef.current.abort();
+ setIsLoading(false);
+ }
+ setIsLoading(false);
+ }
+
+ async function startQuery() {
+ const controller = new AbortController();
+ abortControllerRef.current = controller;
+
+ setIsLoading(true);
+ const query = generateEnrichmentQuery(
+ `biolink:${inputNodeType || 'NamedThing'}`,
+ `biolink:${outputType}`,
+ curies,
+ `biolink:${relationship}`,
+ );
+ const { data } = await axios.post('https://answercoalesce.renci.org/query', query, { signal: controller.signal });
+ setResults(extractResultsStructured(data));
+ setIsLoading(false);
+ }
+
+ if (!categories.length || !predicates.length) {
+ return null;
+ }
+
+ return (
+
+
+ Enrichment Analysis
+
+ This tool helps discover common connections between nodes. Given a
+ list of input nodes, a relationship, and an output type, it will
+ return a list of nodes that are best connected to the input nodes
+ via the relationship.
+
+
+
+
+
+
+
+
+
+
+ p.predicate.split(':')[1]).sort()}
+ onChange={setRelationship}
+ value={relationship}
+ />
+ c.split(':')[1]).sort()}
+ onChange={setOutputType}
+ value={outputType}
+ />
+
+
+
+
+ {isLoading ? 'Stop Query' : 'Submit Query'}
+
+
+ {results.length > 0 && (
+ {
+ const jsonToCsvString = (json) => new Promise((res, rej) => {
+ csv.stringify(json, (err, output) => {
+ if (err) rej(err);
+ else res(output);
+ });
+ });
+
+ const csvObj = results.map(({ id, name, p_value }) => [id, name, p_value]);
+ csvObj.unshift(['ID', 'Name', 'P-value']);
+ const csvStr = await jsonToCsvString(csvObj);
+
+ const blob = new Blob([csvStr], { type: 'text/csv' });
+ const a = document.createElement('a');
+ a.download = 'enrichment-analysis.csv';
+ a.href = window.URL.createObjectURL(blob);
+ document.body.appendChild(a);
+ a.click();
+ a.remove();
+ }}
+ >
+ Download results as CSV
+
+ )}
+
+
+ {results.length > 0 && (
+
+
Results
+
+
+
+ ID
+ Name
+ P-value
+
+
+
+ {results
+ .sort((a, b) => a.p_value - b.p_value)
+ .slice(0, 500)
+ .map(({ id, name, p_value }) => (
+
+ {id}
+ {name}
+ {p_value.toFixed(6)}
+
+ ))}
+
+
+
+ )}
+
+
+
+ );
+}
diff --git a/src/pages/EnrichedQueries/NodeInputBox.jsx b/src/pages/EnrichedQueries/NodeInputBox.jsx
new file mode 100644
index 00000000..0b0940b5
--- /dev/null
+++ b/src/pages/EnrichedQueries/NodeInputBox.jsx
@@ -0,0 +1,304 @@
+import { RichTextarea } from 'rich-textarea';
+import React, {
+ forwardRef,
+ useCallback,
+ useEffect,
+ useMemo,
+ useRef,
+ useState,
+} from 'react';
+import {
+ autoUpdate,
+ FloatingFocusManager,
+ FloatingPortal,
+ size,
+ useDismiss,
+ useId,
+ useInteractions,
+ useListNavigation,
+ useRole,
+ flip, useFloating,
+} from '@floating-ui/react';
+
+import { useQuery } from '../../hooks/use-query';
+import nameLookup from './name-resolver';
+
+export default function NodeInputBox({ onCurieListChange, inputNodeTaxa, inputNodeType }) {
+ const [open, setOpen] = useState(false);
+ const [value, setValue] = useState('');
+ const [activeIndex, setActiveIndex] = useState(null);
+ const [validNames, setValidNames] = useState(new Map());
+
+ useEffect(() => {
+ const curies = value
+ .split('\n')
+ .map((line) => validNames.get(line))
+ .filter((line) => line !== undefined);
+ onCurieListChange(curies);
+ }, [value, validNames, onCurieListChange]);
+
+ const [selection, setSelection] = useState({
+ top: 0, left: 0, selectionStart: 0, selectionEnd: 0,
+ });
+
+ const listRef = useRef([]);
+
+ const { refs, floatingStyles, context } = useFloating({
+ whileElementsMounted: autoUpdate,
+ open,
+ onOpenChange: setOpen,
+ placement: 'bottom-start',
+ middleware: [
+ flip(),
+ size({
+ padding: 16,
+ apply({ availableHeight, availableWidth, elements }) {
+ elements.floating.style.maxHeight = `${availableHeight}px`;
+ elements.floating.style.maxWidth = `${availableWidth}px`;
+ },
+ }),
+ ],
+ });
+
+ const role = useRole(context, { role: 'listbox' });
+ const dismiss = useDismiss(context);
+ const listNav = useListNavigation(context, {
+ listRef,
+ activeIndex,
+ onNavigate: setActiveIndex,
+ openOnArrowKeyDown: false,
+ virtual: true,
+ loop: true,
+ });
+
+ const { getReferenceProps, getFloatingProps, getItemProps } = useInteractions(
+ [role, dismiss, listNav],
+ );
+
+ const getCurrentLineIndex = useCallback(
+ () => value.slice(0, selection.selectionStart).split('\n').length - 1,
+ [value, selection],
+ );
+
+ useEffect(() => {
+ refs.setPositionReference({
+ getBoundingClientRect: () => ({
+ x: 0,
+ y: 0,
+ top: selection.top,
+ left: selection.left,
+ bottom: selection.top + 20,
+ right: selection.left,
+ width: 0,
+ height: 20,
+ }),
+ });
+ }, [selection, refs]);
+
+ const currentLineText = useMemo(() => {
+ const currentLineIndex = getCurrentLineIndex();
+ return value.split('\n')[currentLineIndex];
+ }, [getCurrentLineIndex, value]);
+
+ const {
+ data: options,
+ isLoading,
+ } = useQuery({
+ queryFn: async (signal) => {
+ if (currentLineText.length === 0) return [];
+ return nameLookup({
+ signal,
+ name: currentLineText,
+ taxaFilter: inputNodeTaxa.trim().split(',').map(((t) => t.trim())),
+ biolinkTypeFilter: inputNodeType,
+ });
+ },
+ debounceMs: 250,
+ queryKey: `${currentLineText}-${inputNodeTaxa}-${inputNodeType}`,
+ keepStaleData: true,
+ });
+
+ function handleSelectItem() {
+ setActiveIndex(null);
+ setOpen(false);
+
+ if (!options || options.length === 0 || activeIndex === null) return;
+
+ const selectedOption = options[activeIndex];
+
+ setValidNames((prev) => {
+ const nextMap = new Map(prev);
+ nextMap.set(selectedOption.label, selectedOption.curie);
+ return nextMap;
+ });
+
+ setValue((prev) => {
+ const lines = prev.split('\n');
+ const currentLineIndex = getCurrentLineIndex();
+ lines[currentLineIndex] = selectedOption.label;
+ return lines.join('\n');
+ });
+ }
+
+ return (
+
+ {/* REFERENCE */}
+
+ Input nodes
+
+
{
+ setValue(e.target.value);
+ },
+ 'aria-autocomplete': 'list',
+ onKeyDown: (e) => {
+ if (open) {
+ if (e.key === 'Enter') {
+ e.preventDefault();
+ handleSelectItem();
+ }
+ }
+
+ const noModifiers = !e.ctrlKey && !e.altKey && !e.metaKey;
+
+ if (
+ (e.ctrlKey && e.code === 'Space') ||
+ (noModifiers && e.key.length === 1 && e.key.match(/\S| /))
+ ) {
+ setActiveIndex(0);
+ setOpen(true);
+ }
+ },
+ })}
+ >
+ {(content) => content.split('\n').map((line, i) => (
+
+
+ {`${line}\n`}
+
+
+ ))}
+
+
+ {/* FLOATING */}
+ {open && (
+
+
+
+ {isLoading && (
+
+ Loading…
+
+ )}
+ {options === null || (options.length === 0 && !isLoading) ? (
+
+ No matching results, please try a different query
+
+ ) : (
+ <>
+ {Boolean(options) && options.map((option, i) => (
+
-
+
+ {option.label}
+
+ {option.curie}
+
+
+
+ ))}
+
+ )}
+
+
+ )}
+
+ {children}
+
+ );
+ },
+ ),
+);
diff --git a/src/pages/EnrichedQueries/Select.jsx b/src/pages/EnrichedQueries/Select.jsx
new file mode 100644
index 00000000..b2d8037e
--- /dev/null
+++ b/src/pages/EnrichedQueries/Select.jsx
@@ -0,0 +1,45 @@
+import React from 'react';
+
+export default function Select({
+ options,
+ onChange,
+ value,
+ label,
+ notSelectedOption,
+}) {
+ return (
+
+
+ {label}
+
+ {
+ const v = e.target.value;
+ onChange(v === notSelectedOption ? undefined : v);
+ }}
+ >
+ {(notSelectedOption ? [notSelectedOption, ...options] : options).map((option) => (
+
+ {option}
+
+ ))}
+
+
+ );
+}
diff --git a/src/pages/EnrichedQueries/name-resolver.js b/src/pages/EnrichedQueries/name-resolver.js
new file mode 100644
index 00000000..711a2adf
--- /dev/null
+++ b/src/pages/EnrichedQueries/name-resolver.js
@@ -0,0 +1,23 @@
+import axios from 'axios';
+
+export default async function nameLookup({
+ name,
+ limit = 100,
+ biolinkTypeFilter,
+ taxaFilter,
+ signal,
+}) {
+ const { data } = await axios.get('https://robokop-name-resolver.apps.renci.org/lookup', {
+ signal,
+ params: {
+ string: name,
+ autocomplete: true,
+ offset: 0,
+ limit,
+ biolink_type: biolinkTypeFilter,
+ only_taxa: (taxaFilter || []).join('|') || undefined,
+ },
+ });
+
+ return data;
+}
diff --git a/src/pages/explore/Explore.jsx b/src/pages/explore/Explore.jsx
index 90944cb4..a87906bb 100644
--- a/src/pages/explore/Explore.jsx
+++ b/src/pages/explore/Explore.jsx
@@ -6,6 +6,7 @@ import {
Switch, Route, Link, useRouteMatch,
} from 'react-router-dom';
import DrugChemicalPairs from './DrugDiseasePairs';
+import EnrichedQueries from '../EnrichedQueries/EnrichedQueries';
export default function Explore() {
const match = useRouteMatch();
@@ -15,6 +16,9 @@ export default function Explore() {
+
+
@@ -31,20 +35,37 @@ function Index() {
Explore
- Click a link below to view a curated dataset that can be further explored in the ROBOKOP query builder or answer explorer.
+ Click a link below to view a tool or a curated dataset that can be further explored in the ROBOKOP query builder or answer explorer.
- 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”.
-
+
+
+ Enrichment Analysis{' '}
+
+ Tool
+
+
+
+ This tool allows you to query the ROBOKOP knowledge graph using a list of nodes.
+
+
+
+ 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”.
+
+