diff --git a/package-lock.json b/package-lock.json
index bc2336916ca4fc3ad3c54345e72f2f28a4911655..64a09fbcce6fe4f26912b71b09e63e9f89375076 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -5,9 +5,9 @@
"requires": true,
"dependencies": {
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- "version": "12.1.0",
- "resolved": "https://registry.npmjs.org/@angular-builders/custom-webpack/-/custom-webpack-12.1.0.tgz",
- "integrity": "sha512-7tq0q4PN0L3rTTRxWz5f9xWGt2duYCutDhuRc6Rac6yG13SiTirawqUg2ROx0T3qFjo2G8IWzAageIEzHjl5DA==",
+ "version": "12.1.3",
+ "resolved": "https://registry.npmjs.org/@angular-builders/custom-webpack/-/custom-webpack-12.1.3.tgz",
+ "integrity": "sha512-CzOkwYnO2Xs+z4kMeJkUALeRjVE69SlrqbEsv2Tao5PsBmFCyT5EEVoSvwOuaxZmajuGaXtz7yBIeK2hYp25/A==",
"dev": true,
"requires": {
"@angular-devkit/architect": ">=0.1200.0 < 0.1300.0",
@@ -20,12 +20,12 @@
}
},
"@angular-devkit/architect": {
- "version": "0.1200.3",
- "resolved": "https://registry.npmjs.org/@angular-devkit/architect/-/architect-0.1200.3.tgz",
- "integrity": "sha512-CaqushsPYQ3Us7eBIuZM9/u5H6Rjvm5tUCYS7D5lr5w4QbiwC+6L4dheWEu1PuS2TyyBt6lVwgUNguOmixDb0Q==",
+ "version": "0.1202.17",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/architect/-/architect-0.1202.17.tgz",
+ "integrity": "sha512-uUQcHcLbPvr9adALQSLU1MTDduVUR2kZAHi2e7SmL9ioel84pPVXBoD0WpSBeUMKwPiDs3TQDaxDB49hl0nBSQ==",
"dev": true,
"requires": {
- "@angular-devkit/core": "12.0.3",
+ "@angular-devkit/core": "12.2.17",
"rxjs": "6.6.7"
},
"dependencies": {
@@ -47,15 +47,15 @@
}
},
"@angular-devkit/build-angular": {
- "version": "12.0.3",
- "resolved": "https://registry.npmjs.org/@angular-devkit/build-angular/-/build-angular-12.0.3.tgz",
- "integrity": "sha512-zSQaWT64Nr+vMNNJ6JRFMA8ryNUhx9/kBUR5/s5HP43Y68nLw6EjdUryE5c8tIem+Pc+TcnHpZb9/q4d5VumCQ==",
+ "version": "12.0.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/build-angular/-/build-angular-12.0.5.tgz",
+ "integrity": "sha512-rFbaAQPeuWM9KE9lK3J0sF6GB9nKF/s2Z7rtzKux7whGTF3Tlj8NHrcSxZTf4eBm3cnEpaiod1uPBQg8fUWD4w==",
"dev": true,
"requires": {
- "@angular-devkit/architect": "0.1200.3",
- "@angular-devkit/build-optimizer": "0.1200.3",
- "@angular-devkit/build-webpack": "0.1200.3",
- "@angular-devkit/core": "12.0.3",
+ "@angular-devkit/architect": "0.1200.5",
+ "@angular-devkit/build-optimizer": "0.1200.5",
+ "@angular-devkit/build-webpack": "0.1200.5",
+ "@angular-devkit/core": "12.0.5",
"@babel/core": "7.14.3",
"@babel/generator": "7.14.3",
"@babel/plugin-transform-async-to-generator": "7.13.0",
@@ -65,7 +65,7 @@
"@babel/template": "7.12.13",
"@discoveryjs/json-ext": "0.5.2",
"@jsdevtools/coverage-istanbul-loader": "3.0.5",
- "@ngtools/webpack": "12.0.3",
+ "@ngtools/webpack": "12.0.5",
"ansi-colors": "4.1.1",
"babel-loader": "8.2.2",
"browserslist": "^4.9.1",
@@ -114,20 +114,86 @@
"terser-webpack-plugin": "5.1.2",
"text-table": "0.2.0",
"tree-kill": "1.2.2",
- "webpack": "5.38.1",
+ "webpack": "5.39.1",
"webpack-dev-middleware": "4.1.0",
"webpack-dev-server": "3.11.2",
"webpack-merge": "5.7.3",
"webpack-subresource-integrity": "1.5.2"
},
"dependencies": {
- "agent-base": {
- "version": "6.0.2",
- "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz",
- "integrity": "sha512-RZNwNclF7+MS/8bDg70amg32dyeZGZxiDuQmZxKLAlQjr3jGyLx+4Kkk58UO7D2QdgFIQCovuSuZESne6RG6XQ==",
+ "@angular-devkit/architect": {
+ "version": "0.1200.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/architect/-/architect-0.1200.5.tgz",
+ "integrity": "sha512-222VZ4OeaDK3vON8V5m+w15SRWfUs5uOb4H9ij/H9/6tyHD83uWfCDoOGg+ax4wJVdWEFJIS+Vn4ijGcZCq9WQ==",
+ "dev": true,
+ "requires": {
+ "@angular-devkit/core": "12.0.5",
+ "rxjs": "6.6.7"
+ }
+ },
+ "@angular-devkit/core": {
+ "version": "12.0.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/core/-/core-12.0.5.tgz",
+ "integrity": "sha512-zVSQV+8/vjUjsUKGlj8Kf5LioA6AXJTGI0yhHW9q1dFX4dPpbW63k0R1UoIB2wJ0F/AbYVgpnPGPe9BBm2fvZA==",
+ "dev": true,
+ "requires": {
+ "ajv": "8.2.0",
+ "ajv-formats": "2.0.2",
+ "fast-json-stable-stringify": "2.1.0",
+ "magic-string": "0.25.7",
+ "rxjs": "6.6.7",
+ "source-map": "0.7.3"
+ }
+ },
+ "@babel/generator": {
+ "version": "7.14.3",
+ "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.14.3.tgz",
+ "integrity": "sha512-bn0S6flG/j0xtQdz3hsjJ624h3W0r3llttBMfyHX3YrZ/KtLYr15bjA0FXkgW7FpvrDuTuElXeVjiKlYRpnOFA==",
+ "dev": true,
+ "requires": {
+ "@babel/types": "^7.14.2",
+ "jsesc": "^2.5.1",
+ "source-map": "^0.5.0"
+ },
+ "dependencies": {
+ "source-map": {
+ "version": "0.5.7",
+ "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.5.7.tgz",
+ "integrity": "sha512-LbrmJOMUSdEVxIKvdcJzQC+nQhe8FUZQTXQy6+I75skNgn3OoQ0DZA8YnFa7gp8tqtL3KPf1kmo0R5DoApeSGQ==",
+ "dev": true
+ }
+ }
+ },
+ "@babel/template": {
+ "version": "7.12.13",
+ "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.12.13.tgz",
+ "integrity": "sha512-/7xxiGA57xMo/P2GVvdEumr8ONhFOhfgq2ihK3h1e6THqzTAkHbkXgB0xI9yeTfIUoH3+oAeHhqm/I43OTbbjA==",
"dev": true,
"requires": {
- "debug": "4"
+ "@babel/code-frame": "^7.12.13",
+ "@babel/parser": "^7.12.13",
+ "@babel/types": "^7.12.13"
+ }
+ },
+ "ajv": {
+ "version": "8.2.0",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.2.0.tgz",
+ "integrity": "sha512-WSNGFuyWd//XO8n/m/EaOlNLtO0yL8EXT/74LqT4khdhpZjP7lkj/kT5uwRmGitKEVp/Oj7ZUHeGfPtgHhQ5CA==",
+ "dev": true,
+ "requires": {
+ "fast-deep-equal": "^3.1.1",
+ "json-schema-traverse": "^1.0.0",
+ "require-from-string": "^2.0.2",
+ "uri-js": "^4.2.2"
+ }
+ },
+ "ajv-formats": {
+ "version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/ajv-formats/-/ajv-formats-2.0.2.tgz",
+ "integrity": "sha512-Brah4Uo5/U8v76c6euTwtjVFFaVishwnJrQBYpev1JRh4vjA1F4HY3UzQez41YUCszUCXKagG8v6eVRBHV1gkw==",
+ "dev": true,
+ "requires": {
+ "ajv": "^8.0.0"
}
},
"glob": {
@@ -144,16 +210,6 @@
"path-is-absolute": "^1.0.0"
}
},
- "https-proxy-agent": {
- "version": "5.0.0",
- "resolved": "https://registry.npmjs.org/https-proxy-agent/-/https-proxy-agent-5.0.0.tgz",
- "integrity": "sha512-EkYm5BcKUGiduxzSt3Eppko+PiNWNEpa4ySk9vTC6wDsQJW9rHSa+UhGNJoRYp7bz6Ht1eaRIa6QaJqO5rCFbA==",
- "dev": true,
- "requires": {
- "agent-base": "6",
- "debug": "4"
- }
- },
"postcss": {
"version": "8.3.0",
"resolved": "https://registry.npmjs.org/postcss/-/postcss-8.3.0.tgz",
@@ -165,28 +221,6 @@
"source-map-js": "^0.6.2"
}
},
- "postcss-import": {
- "version": "14.0.1",
- "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-14.0.1.tgz",
- "integrity": "sha512-Xn2+z++vWObbEPhiiKO1a78JiyhqipyrXHBb3AHpv0ks7Cdg+GxQQJ24ODNMTanldf7197gSP3axppO9yaG0lA==",
- "dev": true,
- "requires": {
- "postcss-value-parser": "^4.0.0",
- "read-cache": "^1.0.0",
- "resolve": "^1.1.7"
- }
- },
- "postcss-loader": {
- "version": "5.2.0",
- "resolved": "https://registry.npmjs.org/postcss-loader/-/postcss-loader-5.2.0.tgz",
- "integrity": "sha512-uSuCkENFeUaOYsKrXm0eNNgVIxc71z8RcckLMbVw473rGojFnrUeqEz6zBgXsH2q1EIzXnO/4pEz9RhALjlITA==",
- "dev": true,
- "requires": {
- "cosmiconfig": "^7.0.0",
- "klona": "^2.0.4",
- "semver": "^7.3.4"
- }
- },
"rxjs": {
"version": "6.6.7",
"resolved": "https://registry.npmjs.org/rxjs/-/rxjs-6.6.7.tgz",
@@ -196,70 +230,90 @@
"tslib": "^1.9.0"
}
},
- "semver": {
- "version": "7.3.5",
- "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.5.tgz",
- "integrity": "sha512-PoeGJYh8HK4BTO/a9Tf6ZG3veo/A7ZVsYrSA6J8ny9nb3B1VrpkuN+z9OE5wfE5p6H4LchYZsegiQgbJD94ZFQ==",
- "dev": true,
- "requires": {
- "lru-cache": "^6.0.0"
- }
- },
- "source-map-support": {
- "version": "0.5.19",
- "resolved": "https://registry.npmjs.org/source-map-support/-/source-map-support-0.5.19.tgz",
- "integrity": "sha512-Wonm7zOCIJzBGQdB+thsPar0kYuCIzYvxZwlBa87yi/Mdjv7Tip2cyVbLj5o0cFPN4EVkuTwb3GDDyUx2DGnGw==",
- "dev": true,
- "requires": {
- "buffer-from": "^1.0.0",
- "source-map": "^0.6.0"
- },
- "dependencies": {
- "source-map": {
- "version": "0.6.1",
- "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz",
- "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==",
- "dev": true
- }
- }
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"tslib": {
"version": "1.14.1",
"resolved": "https://registry.npmjs.org/tslib/-/tslib-1.14.1.tgz",
"integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==",
"dev": true
+ },
+ "webpack-merge": {
+ "version": "5.7.3",
+ "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.7.3.tgz",
+ "integrity": "sha512-6/JUQv0ELQ1igjGDzHkXbVDRxkfA57Zw7PfiupdLFJYrgFqY5ZP8xxbpp2lU3EPwYx89ht5Z/aDkD40hFCm5AA==",
+ "dev": true,
+ "requires": {
+ "clone-deep": "^4.0.1",
+ "wildcard": "^2.0.0"
+ }
}
}
},
"@angular-devkit/build-optimizer": {
- "version": "0.1200.3",
- "resolved": "https://registry.npmjs.org/@angular-devkit/build-optimizer/-/build-optimizer-0.1200.3.tgz",
- "integrity": "sha512-GELr5FTkwLJrTuARfTnBn+NkJjGbmbqrm/+znU6QlhyOTSE/PNZed0kiiTP68BQtL4FO5SeTcJ3tdjOW8i3hiw==",
+ "version": "0.1200.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/build-optimizer/-/build-optimizer-0.1200.5.tgz",
+ "integrity": "sha512-3XlDVVak3CfIgUjDZMoON7sxnI1vxhzEm2LvVg5yN98Q7ijnfykXiIzryEcplzTMTZwGNkem0361HDs1EX8zNg==",
"dev": true,
"requires": {
"source-map": "0.7.3",
"tslib": "2.2.0",
"typescript": "4.2.4"
- },
- "dependencies": {
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- "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.2.4.tgz",
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- "dev": true
- }
}
},
"@angular-devkit/build-webpack": {
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- "resolved": "https://registry.npmjs.org/@angular-devkit/build-webpack/-/build-webpack-0.1200.3.tgz",
- "integrity": "sha512-RVQ9+mBRnxn1si/q2aMzpnXOXMv1a64nNrhNqP4n43jczZW1Cu85TnwYxeTjXnR3I5u+7wtpifqi9H3pLxV7lQ==",
+ "version": "0.1200.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/build-webpack/-/build-webpack-0.1200.5.tgz",
+ "integrity": "sha512-cx8DVwOmogzeHS1dsZGWummwA3T1zqsJ6q9NIL0S0ZiOScZuz0j9zAOLjBkyCj5XexOFzHv3TcAVQyzJsi1tIw==",
"dev": true,
"requires": {
- "@angular-devkit/architect": "0.1200.3",
+ "@angular-devkit/architect": "0.1200.5",
"rxjs": "6.6.7"
},
"dependencies": {
+ "@angular-devkit/architect": {
+ "version": "0.1200.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/architect/-/architect-0.1200.5.tgz",
+ "integrity": "sha512-222VZ4OeaDK3vON8V5m+w15SRWfUs5uOb4H9ij/H9/6tyHD83uWfCDoOGg+ax4wJVdWEFJIS+Vn4ijGcZCq9WQ==",
+ "dev": true,
+ "requires": {
+ "@angular-devkit/core": "12.0.5",
+ "rxjs": "6.6.7"
+ }
+ },
+ "@angular-devkit/core": {
+ "version": "12.0.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/core/-/core-12.0.5.tgz",
+ "integrity": "sha512-zVSQV+8/vjUjsUKGlj8Kf5LioA6AXJTGI0yhHW9q1dFX4dPpbW63k0R1UoIB2wJ0F/AbYVgpnPGPe9BBm2fvZA==",
+ "dev": true,
+ "requires": {
+ "ajv": "8.2.0",
+ "ajv-formats": "2.0.2",
+ "fast-json-stable-stringify": "2.1.0",
+ "magic-string": "0.25.7",
+ "rxjs": "6.6.7",
+ "source-map": "0.7.3"
+ }
+ },
+ "ajv": {
+ "version": "8.2.0",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.2.0.tgz",
+ "integrity": "sha512-WSNGFuyWd//XO8n/m/EaOlNLtO0yL8EXT/74LqT4khdhpZjP7lkj/kT5uwRmGitKEVp/Oj7ZUHeGfPtgHhQ5CA==",
+ "dev": true,
+ "requires": {
+ "fast-deep-equal": "^3.1.1",
+ "json-schema-traverse": "^1.0.0",
+ "require-from-string": "^2.0.2",
+ "uri-js": "^4.2.2"
+ }
+ },
+ "ajv-formats": {
+ "version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/ajv-formats/-/ajv-formats-2.0.2.tgz",
+ "integrity": "sha512-Brah4Uo5/U8v76c6euTwtjVFFaVishwnJrQBYpev1JRh4vjA1F4HY3UzQez41YUCszUCXKagG8v6eVRBHV1gkw==",
+ "dev": true,
+ "requires": {
+ "ajv": "^8.0.0"
+ }
+ },
"rxjs": {
"version": "6.6.7",
"resolved": "https://registry.npmjs.org/rxjs/-/rxjs-6.6.7.tgz",
@@ -278,49 +332,19 @@
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"@angular-devkit/core": {
- "version": "12.0.3",
- "resolved": "https://registry.npmjs.org/@angular-devkit/core/-/core-12.0.3.tgz",
- "integrity": "sha512-d6E4ldHzIerzFpXXZkynluIbZZeYD+VteFLBZ77lOXAuUYuuLEiW8h4bpJOqribeJli5c1cJ/yyELYHrbiiLcw==",
+ "version": "12.2.17",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/core/-/core-12.2.17.tgz",
+ "integrity": "sha512-PyOY7LGUPPd6rakxUYbfQN6zAdOCMCouVp5tERY1WTdMdEiuULOtHsPee8kNbh75pD59KbJNU+fwozPRMuIm5g==",
"dev": true,
"requires": {
- "ajv": "8.2.0",
- "ajv-formats": "2.0.2",
+ "ajv": "8.6.2",
+ "ajv-formats": "2.1.0",
"fast-json-stable-stringify": "2.1.0",
"magic-string": "0.25.7",
"rxjs": "6.6.7",
"source-map": "0.7.3"
},
"dependencies": {
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- "version": "8.2.0",
- "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.2.0.tgz",
- "integrity": "sha512-WSNGFuyWd//XO8n/m/EaOlNLtO0yL8EXT/74LqT4khdhpZjP7lkj/kT5uwRmGitKEVp/Oj7ZUHeGfPtgHhQ5CA==",
- "dev": true,
- "requires": {
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- "json-schema-traverse": "^1.0.0",
- "require-from-string": "^2.0.2",
- "uri-js": "^4.2.2"
- }
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- "fast-deep-equal": {
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- "resolved": "https://registry.npmjs.org/fast-deep-equal/-/fast-deep-equal-3.1.3.tgz",
- "integrity": "sha512-f3qQ9oQy9j2AhBe/H9VC91wLmKBCCU/gDOnKNAYG5hswO7BLKj09Hc5HYNz9cGI++xlpDCIgDaitVs03ATR84Q==",
- "dev": true
- },
- "fast-json-stable-stringify": {
- "version": "2.1.0",
- "resolved": "https://registry.npmjs.org/fast-json-stable-stringify/-/fast-json-stable-stringify-2.1.0.tgz",
- "integrity": "sha512-lhd/wF+Lk98HZoTCtlVraHtfh5XYijIjalXck7saUtuanSDyLMxnHhSXEDJqHxD7msR8D0uCmqlkwjCV8xvwHw==",
- "dev": true
- },
- "json-schema-traverse": {
- "version": "1.0.0",
- "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz",
- "integrity": "sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug==",
- "dev": true
- },
"rxjs": {
"version": "6.6.7",
"resolved": "https://registry.npmjs.org/rxjs/-/rxjs-6.6.7.tgz",
@@ -339,16 +363,51 @@
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},
"@angular-devkit/schematics": {
- "version": "12.0.3",
- "resolved": "https://registry.npmjs.org/@angular-devkit/schematics/-/schematics-12.0.3.tgz",
- "integrity": "sha512-FozSvAJPI1iNLkrMVfbQvrk6XxF86zkpnVoaOeT/S2WeS64uRLW9DZmFHJxD4K2+MUPkwx6x6Y8AjARIkGtcIA==",
+ "version": "12.0.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/schematics/-/schematics-12.0.5.tgz",
+ "integrity": "sha512-iW3XuDHScr3TXuunlEjF5O01zBpwpLgfr1oEny8PvseFGDlHK4Nj8zNIoIn3Yg936aiFO4GJAC/UXsT8g5vKxQ==",
"dev": true,
"requires": {
- "@angular-devkit/core": "12.0.3",
+ "@angular-devkit/core": "12.0.5",
"ora": "5.4.0",
"rxjs": "6.6.7"
},
"dependencies": {
+ "@angular-devkit/core": {
+ "version": "12.0.5",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/core/-/core-12.0.5.tgz",
+ "integrity": "sha512-zVSQV+8/vjUjsUKGlj8Kf5LioA6AXJTGI0yhHW9q1dFX4dPpbW63k0R1UoIB2wJ0F/AbYVgpnPGPe9BBm2fvZA==",
+ "dev": true,
+ "requires": {
+ "ajv": "8.2.0",
+ "ajv-formats": "2.0.2",
+ "fast-json-stable-stringify": "2.1.0",
+ "magic-string": "0.25.7",
+ "rxjs": "6.6.7",
+ "source-map": "0.7.3"
+ }
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+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+ "integrity": "sha512-VhumSSbBqDTP8p2ZLKj40UjBCV4+v8bUSEpUb4KjRgWk9pbqGF4REFj6KEagidb2f/M6AzC0EmFyDNGaw9OCzg==",
+ "dev": true,
+ "requires": {
+ "ansi-regex": "^2.0.0"
}
},
"supports-color": {
@@ -14236,7 +14418,7 @@
"to-regex-range": {
"version": "2.1.1",
"resolved": "https://registry.npmjs.org/to-regex-range/-/to-regex-range-2.1.1.tgz",
- "integrity": "sha1-fIDBe53+vlmeJzZ+DU3VWQFB2zg=",
+ "integrity": "sha512-ZZWNfCjUokXXDGXFpZehJIkZqq91BcULFq/Pi7M5i4JnxXdhMKAK682z8bCW3o8Hj1wuuzoKcW3DfVzaP6VuNg==",
"dev": true,
"requires": {
"is-number": "^3.0.0",
@@ -14255,56 +14437,6 @@
"range-parser": "^1.2.1",
"webpack-log": "^2.0.0"
}
- },
- "wrap-ansi": {
- "version": "5.1.0",
- "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-5.1.0.tgz",
- "integrity": "sha512-QC1/iN/2/RPVJ5jYK8BGttj5z83LmSKmvbvrXPNCLZSEb32KKVDJDl/MOt2N01qU2H/FkzEa9PKto1BqDjtd7Q==",
- "dev": true,
- "requires": {
- "ansi-styles": "^3.2.0",
- "string-width": "^3.0.0",
- "strip-ansi": "^5.0.0"
- },
- "dependencies": {
- "strip-ansi": {
- "version": "5.2.0",
- "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz",
- "integrity": "sha512-DuRs1gKbBqsMKIZlrffwlug8MHkcnpjs5VPmL1PAh+mA30U0DTotfDZ0d2UUsXpPmPmMMJ6W773MaA3J+lbiWA==",
- "dev": true,
- "requires": {
- "ansi-regex": "^4.1.0"
- }
- }
- }
- },
- "yargs": {
- "version": "13.3.2",
- "resolved": "https://registry.npmjs.org/yargs/-/yargs-13.3.2.tgz",
- "integrity": "sha512-AX3Zw5iPruN5ie6xGRIDgqkT+ZhnRlZMLMHAs8tg7nRruy2Nb+i5o9bwghAogtM08q1dpr2LVoS8KSTMYpWXUw==",
- "dev": true,
- "requires": {
- "cliui": "^5.0.0",
- "find-up": "^3.0.0",
- "get-caller-file": "^2.0.1",
- "require-directory": "^2.1.1",
- "require-main-filename": "^2.0.0",
- "set-blocking": "^2.0.0",
- "string-width": "^3.0.0",
- "which-module": "^2.0.0",
- "y18n": "^4.0.0",
- "yargs-parser": "^13.1.2"
- }
- },
- "yargs-parser": {
- "version": "13.1.2",
- "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz",
- "integrity": "sha512-3lbsNRf/j+A4QuSZfDRA7HRSfWrzO0YjqTJd5kjAq37Zep1CEgaYmrH9Q3GwPiB9cHyd1Y1UwggGhJGoxipbzg==",
- "dev": true,
- "requires": {
- "camelcase": "^5.0.0",
- "decamelize": "^1.2.0"
- }
}
}
},
@@ -14323,13 +14455,19 @@
"resolved": "https://registry.npmjs.org/ansi-colors/-/ansi-colors-3.2.4.tgz",
"integrity": "sha512-hHUXGagefjN2iRrID63xckIvotOXOojhQKWIPUZ4mNUZ9nLZW+7FMNoE1lOkEhNWYsx/7ysGIuJYCiMAA9FnrA==",
"dev": true
+ },
+ "uuid": {
+ "version": "3.4.0",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-3.4.0.tgz",
+ "integrity": "sha512-HjSDRw6gZE5JMggctHBcjVak08+KEVhSIiDzFnT9S9aegmp85S/bReBVTb4QTFaRNptJ9kuYaNhnbNEOkbKb/A==",
+ "dev": true
}
}
},
"webpack-merge": {
- "version": "5.7.3",
- "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.7.3.tgz",
- "integrity": "sha512-6/JUQv0ELQ1igjGDzHkXbVDRxkfA57Zw7PfiupdLFJYrgFqY5ZP8xxbpp2lU3EPwYx89ht5Z/aDkD40hFCm5AA==",
+ "version": "5.8.0",
+ "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.8.0.tgz",
+ "integrity": "sha512-/SaI7xY0831XwP6kzuwhKWVKDP9t1QY1h65lAFLbZqMPIuYcD9QAW4u9STIbU9kaJbPBB/geU/gLr1wDjOhQ+Q==",
"dev": true,
"requires": {
"clone-deep": "^4.0.1",
@@ -14392,43 +14530,16 @@
"which-module": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/which-module/-/which-module-2.0.0.tgz",
- "integrity": "sha1-2e8H3Od7mQK4o6j6SzHD4/fm6Ho=",
+ "integrity": "sha512-B+enWhmw6cjfVC7kS8Pj9pCrKSc5txArRyaYGe088shv/FGWH+0Rjx/xPgtsWfsUtS27FkP697E4DDhgrgoc0Q==",
"dev": true
},
"wide-align": {
- "version": "1.1.3",
- "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.3.tgz",
- "integrity": "sha512-QGkOQc8XL6Bt5PwnsExKBPuMKBxnGxWWW3fU55Xt4feHozMUhdUMaBCk290qpm/wG5u/RSKzwdAC4i51YigihA==",
+ "version": "1.1.5",
+ "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.5.tgz",
+ "integrity": "sha512-eDMORYaPNZ4sQIuuYPDHdQvf4gyCF9rEEV/yPxGfwPkRodwEgiMUUXTx/dex+Me0wxx53S+NgUHaP7y3MGlDmg==",
"dev": true,
"requires": {
- "string-width": "^1.0.2 || 2"
- },
- "dependencies": {
- "ansi-regex": {
- "version": "3.0.0",
- "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-3.0.0.tgz",
- "integrity": "sha1-7QMXwyIGT3lGbAKWa922Bas32Zg=",
- "dev": true
- },
- "string-width": {
- "version": "2.1.1",
- "resolved": "https://registry.npmjs.org/string-width/-/string-width-2.1.1.tgz",
- "integrity": "sha512-nOqH59deCq9SRHlxq1Aw85Jnt4w6KvLKqWVik6oA9ZklXLNIOlqg4F2yrT1MVaTjAqvVwdfeZ7w7aCvJD7ugkw==",
- "dev": true,
- "requires": {
- "is-fullwidth-code-point": "^2.0.0",
- "strip-ansi": "^4.0.0"
- }
- },
- "strip-ansi": {
- "version": "4.0.0",
- "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-4.0.0.tgz",
- "integrity": "sha1-qEeQIusaw2iocTibY1JixQXuNo8=",
- "dev": true,
- "requires": {
- "ansi-regex": "^3.0.0"
- }
- }
+ "string-width": "^1.0.2 || 2 || 3 || 4"
}
},
"wildcard": {
@@ -14438,53 +14549,46 @@
"dev": true
},
"wrap-ansi": {
- "version": "6.2.0",
- "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-6.2.0.tgz",
- "integrity": "sha512-r6lPcBGxZXlIcymEu7InxDMhdW0KDxpLgoFLcguasxCaJ/SOIZwINatK9KY/tf+ZrlywOKU0UDj3ATXUBfxJXA==",
+ "version": "5.1.0",
+ "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-5.1.0.tgz",
+ "integrity": "sha512-QC1/iN/2/RPVJ5jYK8BGttj5z83LmSKmvbvrXPNCLZSEb32KKVDJDl/MOt2N01qU2H/FkzEa9PKto1BqDjtd7Q==",
"dev": true,
"requires": {
- "ansi-styles": "^4.0.0",
- "string-width": "^4.1.0",
- "strip-ansi": "^6.0.0"
+ "ansi-styles": "^3.2.0",
+ "string-width": "^3.0.0",
+ "strip-ansi": "^5.0.0"
},
"dependencies": {
"ansi-regex": {
- "version": "5.0.0",
- "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.0.tgz",
- "integrity": "sha512-bY6fj56OUQ0hU1KjFNDQuJFezqKdrAyFdIevADiqrWHwSlbmBNMHp5ak2f40Pm8JTFyM2mqxkG6ngkHO11f/lg==",
+ "version": "4.1.1",
+ "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.1.1.tgz",
+ "integrity": "sha512-ILlv4k/3f6vfQ4OoP2AGvirOktlQ98ZEL1k9FaQjxa3L1abBgbuTDAdPOpvbGncC0BTVQrl+OM8xZGK6tWXt7g==",
"dev": true
},
- "ansi-styles": {
- "version": "4.3.0",
- "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
- "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
- "dev": true,
- "requires": {
- "color-convert": "^2.0.1"
- }
+ "emoji-regex": {
+ "version": "7.0.3",
+ "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-7.0.3.tgz",
+ "integrity": "sha512-CwBLREIQ7LvYFB0WyRvwhq5N5qPhc6PMjD6bYggFlI5YyDgl+0vxq5VHbMOFqLg7hfWzmu8T5Z1QofhmTIhItA==",
+ "dev": true
},
- "color-convert": {
- "version": "2.0.1",
- "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
- "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
+ "string-width": {
+ "version": "3.1.0",
+ "resolved": "https://registry.npmjs.org/string-width/-/string-width-3.1.0.tgz",
+ "integrity": "sha512-vafcv6KjVZKSgz06oM/H6GDBrAtz8vdhQakGjFIvNrHA6y3HCF1CInLy+QLq8dTJPQ1b+KDUqDFctkdRW44e1w==",
"dev": true,
"requires": {
- "color-name": "~1.1.4"
+ "emoji-regex": "^7.0.1",
+ "is-fullwidth-code-point": "^2.0.0",
+ "strip-ansi": "^5.1.0"
}
},
- "color-name": {
- "version": "1.1.4",
- "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
- "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
- "dev": true
- },
"strip-ansi": {
- "version": "6.0.0",
- "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.0.tgz",
- "integrity": "sha512-AuvKTrTfQNYNIctbR1K/YGTR1756GycPsg7b9bdV9Duqur4gv6aKqHXah67Z8ImS7WEz5QVcOtlfW2rZEugt6w==",
+ "version": "5.2.0",
+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz",
+ "integrity": "sha512-DuRs1gKbBqsMKIZlrffwlug8MHkcnpjs5VPmL1PAh+mA30U0DTotfDZ0d2UUsXpPmPmMMJ6W773MaA3J+lbiWA==",
"dev": true,
"requires": {
- "ansi-regex": "^5.0.0"
+ "ansi-regex": "^4.1.0"
}
}
}
@@ -14506,7 +14610,7 @@
"xml": {
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/xml/-/xml-1.0.1.tgz",
- "integrity": "sha1-eLpyAgApxbyHuKgaPPzXS0ovweU=",
+ "integrity": "sha512-huCv9IH9Tcf95zuYCsQraZtWnJvBtLVE0QHMOs8bWyZAFZNDcYjsPq1nEx8jKA9y+Beo9v+7OBPRisQTjinQMw==",
"dev": true
},
"xml2js": {
@@ -14544,68 +14648,107 @@
"dev": true
},
"yargs": {
- "version": "15.4.1",
- "resolved": "https://registry.npmjs.org/yargs/-/yargs-15.4.1.tgz",
- "integrity": "sha512-aePbxDmcYW++PaqBsJ+HYUFwCdv4LVvdnhBy78E57PIor8/OVvhMrADFFEDh8DHDFRv/O9i3lPhsENjO7QX0+A==",
+ "version": "13.3.2",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-13.3.2.tgz",
+ "integrity": "sha512-AX3Zw5iPruN5ie6xGRIDgqkT+ZhnRlZMLMHAs8tg7nRruy2Nb+i5o9bwghAogtM08q1dpr2LVoS8KSTMYpWXUw==",
"dev": true,
"requires": {
- "cliui": "^6.0.0",
- "decamelize": "^1.2.0",
- "find-up": "^4.1.0",
+ "cliui": "^5.0.0",
+ "find-up": "^3.0.0",
"get-caller-file": "^2.0.1",
"require-directory": "^2.1.1",
"require-main-filename": "^2.0.0",
"set-blocking": "^2.0.0",
- "string-width": "^4.2.0",
+ "string-width": "^3.0.0",
"which-module": "^2.0.0",
"y18n": "^4.0.0",
- "yargs-parser": "^18.1.2"
+ "yargs-parser": "^13.1.2"
},
"dependencies": {
+ "ansi-regex": {
+ "version": "4.1.1",
+ "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.1.1.tgz",
+ "integrity": "sha512-ILlv4k/3f6vfQ4OoP2AGvirOktlQ98ZEL1k9FaQjxa3L1abBgbuTDAdPOpvbGncC0BTVQrl+OM8xZGK6tWXt7g==",
+ "dev": true
+ },
+ "emoji-regex": {
+ "version": "7.0.3",
+ "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-7.0.3.tgz",
+ "integrity": "sha512-CwBLREIQ7LvYFB0WyRvwhq5N5qPhc6PMjD6bYggFlI5YyDgl+0vxq5VHbMOFqLg7hfWzmu8T5Z1QofhmTIhItA==",
+ "dev": true
+ },
"find-up": {
- "version": "4.1.0",
- "resolved": "https://registry.npmjs.org/find-up/-/find-up-4.1.0.tgz",
- "integrity": "sha512-PpOwAdQ/YlXQ2vj8a3h8IipDuYRi3wceVQQGYWxNINccq40Anw7BlsEXCMbt1Zt+OLA6Fq9suIpIWD0OsnISlw==",
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/find-up/-/find-up-3.0.0.tgz",
+ "integrity": "sha512-1yD6RmLI1XBfxugvORwlck6f75tYL+iR0jqwsOrOxMZyGYqUuDhJ0l4AXdO1iX/FTs9cBAMEk1gWSEx1kSbylg==",
"dev": true,
"requires": {
- "locate-path": "^5.0.0",
- "path-exists": "^4.0.0"
+ "locate-path": "^3.0.0"
}
},
"locate-path": {
- "version": "5.0.0",
- "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-5.0.0.tgz",
- "integrity": "sha512-t7hw9pI+WvuwNJXwk5zVHpyhIqzg2qTlklJOf0mVxGSbe3Fp2VieZcduNYjaLDoy6p9uGpQEGWG87WpMKlNq8g==",
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-3.0.0.tgz",
+ "integrity": "sha512-7AO748wWnIhNqAuaty2ZWHkQHRSNfPVIsPIfwEOWO22AmaoVrWavlOcMR5nzTLNYvp36X220/maaRsrec1G65A==",
"dev": true,
"requires": {
- "p-locate": "^4.1.0"
+ "p-locate": "^3.0.0",
+ "path-exists": "^3.0.0"
}
},
"p-locate": {
- "version": "4.1.0",
- "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-4.1.0.tgz",
- "integrity": "sha512-R79ZZ/0wAxKGu3oYMlz8jy/kbhsNrS7SKZ7PxEHBgJ5+F2mtFW2fK2cOtBh1cHYkQsbzFV7I+EoRKe6Yt0oK7A==",
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-3.0.0.tgz",
+ "integrity": "sha512-x+12w/To+4GFfgJhBEpiDcLozRJGegY+Ei7/z0tSLkMmxGZNybVMSfWj9aJn8Z5Fc7dBUNJOOVgPv2H7IwulSQ==",
"dev": true,
"requires": {
- "p-limit": "^2.2.0"
+ "p-limit": "^2.0.0"
}
},
"path-exists": {
- "version": "4.0.0",
- "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz",
- "integrity": "sha512-ak9Qy5Q7jYb2Wwcey5Fpvg2KoAc/ZIhLSLOSBmRmygPsGwkVVt0fZa0qrtMz+m6tJTAHfZQ8FnmB4MG4LWy7/w==",
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-3.0.0.tgz",
+ "integrity": "sha512-bpC7GYwiDYQ4wYLe+FA8lhRjhQCMcQGuSgGGqDkg/QerRWw9CmGRT0iSOVRSZJ29NMLZgIzqaljJ63oaL4NIJQ==",
"dev": true
+ },
+ "string-width": {
+ "version": "3.1.0",
+ "resolved": "https://registry.npmjs.org/string-width/-/string-width-3.1.0.tgz",
+ "integrity": "sha512-vafcv6KjVZKSgz06oM/H6GDBrAtz8vdhQakGjFIvNrHA6y3HCF1CInLy+QLq8dTJPQ1b+KDUqDFctkdRW44e1w==",
+ "dev": true,
+ "requires": {
+ "emoji-regex": "^7.0.1",
+ "is-fullwidth-code-point": "^2.0.0",
+ "strip-ansi": "^5.1.0"
+ }
+ },
+ "strip-ansi": {
+ "version": "5.2.0",
+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz",
+ "integrity": "sha512-DuRs1gKbBqsMKIZlrffwlug8MHkcnpjs5VPmL1PAh+mA30U0DTotfDZ0d2UUsXpPmPmMMJ6W773MaA3J+lbiWA==",
+ "dev": true,
+ "requires": {
+ "ansi-regex": "^4.1.0"
+ }
}
}
},
"yargs-parser": {
- "version": "18.1.3",
- "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-18.1.3.tgz",
- "integrity": "sha512-o50j0JeToy/4K6OZcaQmW6lyXXKhq7csREXcDwk2omFPJEwUNOVtJKvmDr9EI1fAJZUyZcRF7kxGBWmRXudrCQ==",
+ "version": "13.1.2",
+ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz",
+ "integrity": "sha512-3lbsNRf/j+A4QuSZfDRA7HRSfWrzO0YjqTJd5kjAq37Zep1CEgaYmrH9Q3GwPiB9cHyd1Y1UwggGhJGoxipbzg==",
"dev": true,
"requires": {
"camelcase": "^5.0.0",
"decamelize": "^1.2.0"
+ },
+ "dependencies": {
+ "camelcase": {
+ "version": "5.3.1",
+ "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-5.3.1.tgz",
+ "integrity": "sha512-L28STB170nwWS63UjtlEOE3dldQApaJXZkOI1uMFfzf3rRuPegHaHesyee+YxQ+W6SvRDQV6UrdOdRiR153wJg==",
+ "dev": true
+ }
}
},
"yn": {
diff --git a/src/app/app.module.ts b/src/app/app.module.ts
index ca8e0debe4a65f2189194533b40a02e644c155c4..8adf6fe8b46c34e99a6bb097cb2fbe3164f0f8a4 100644
--- a/src/app/app.module.ts
+++ b/src/app/app.module.ts
@@ -15,7 +15,6 @@ import { AnalysisPanelComponent } from './components/analysis-panel/analysis-pan
import { TaskListComponent } from './components/task-list/task-list.component';
import { ToggleComponent } from './components/toggle/toggle.component';
import { InfoTileComponent } from './components/info-tile/info-tile.component';
-import { CustomProteinsComponent } from './dialogs/custom-proteins/custom-proteins.component';
import { DownloadButtonComponent } from './components/network/network-menu/download-button/download-button.component';
import { MatTooltipModule } from '@angular/material/tooltip';
@@ -58,7 +57,6 @@ import { CenterViewInverseComponent } from './components/network/network-menu-le
TaskListComponent,
ToggleComponent,
InfoTileComponent,
- CustomProteinsComponent,
AddExpressedProteinsComponent,
NetworkLegendComponent,
ProtTableComponent,
diff --git a/src/app/components/analysis-panel/analysis-panel.component.ts b/src/app/components/analysis-panel/analysis-panel.component.ts
index 59584070065046c76adedb4adc89366f98a1c843..fa726730583c7d330805f5404c26607b73bb120d 100644
--- a/src/app/components/analysis-panel/analysis-panel.component.ts
+++ b/src/app/components/analysis-panel/analysis-panel.component.ts
@@ -197,12 +197,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.networkHandler.activeNetwork.networkInternal = new vis.Network(container, this.nodeData, options);
- this.tableDrugs = nodes.filter( e => e.drugstoneId && e.drugstoneId.startsWith('d'));
+ this.tableDrugs = nodes.filter( e => e.drugstoneId && e.drugstoneId.drugstoneType === 'drug');
this.tableDrugs.forEach((r) => {
r.rawScore = r.score;
});
- this.tableProteins = nodes.filter( e => e.drugstoneId && e.drugstoneId.startsWith('p'));
+ this.tableProteins = nodes.filter( e => e.drugstoneId && e.drugstoneType === 'protein');
this.tableSelectedProteins = [];
this.tableProteins.forEach((r) => {
r.rawScore = r.score;
@@ -233,7 +233,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
if (nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
- if (node.nodeType === 'drug' || node.drugstoneId === undefined || !node.drugstoneId.startsWith('p')) {
+ if (node.nodeType === 'drug' || node.drugstoneId === undefined || node.drugstoneType !== 'protein') {
return;
}
const wrapper = getWrapperFromNode(node);
@@ -304,12 +304,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// else: selected is null
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
- // let drugType;
- // let drugInTrial;
- // if (node.drugstoneId && node.drugstoneId.startsWith('d')) {
- // drugType = node.status;
- // drugInTrial = node.inTrial;
- // }
const isSeed = this.networkHandler.activeNetwork.highlightSeeds ? this.networkHandler.activeNetwork.seedMap[node.id] : false;
const gradient = (this.networkHandler.activeNetwork.gradientMap !== {}) && (this.networkHandler.activeNetwork.gradientMap[node.id]) ? this.networkHandler.activeNetwork.gradientMap[node.id] : 1.0;
const nodeStyled = NetworkSettings.getNodeStyle(
@@ -401,127 +395,10 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
}
- // public saveAddNodes(nodeList: Node[]) {
- // const existing = this.nodeData.nodes.get().map(n => n.id);
- // const toAdd = nodeList.filter(n => existing.indexOf(n.id) === -1)
- // this.nodeData.nodes.add(toAdd);
- // }
-
- // public saveRemoveDisorders(nodeList: Node[]) {
- // const other = this.adjacentDrugDisorderList === nodeList ? this.adjacentProteinDisorderList : this.adjacentDrugDisorderList
- // if (other == null)
- // this.nodeData.nodes.remove(nodeList);
- // else {
- // const otherIds = other.map(d => d.id);
- // const rest = nodeList.filter(d => otherIds.indexOf(d.id) === -1)
- // this.nodeData.nodes.remove(rest)
- // }
- // }
-
- // public updateAdjacentProteinDisorders(bool: boolean) {
- // this.adjacentDisordersProtein = bool;
- // if (this.adjacentDisordersProtein) {
- // this.netex.adjacentDisorders(this.nodeData.nodes, 'proteins').subscribe(response => {
- // for (const interaction of response.edges) {
- // const edge = {from: interaction.protein, to: interaction.disorder};
- // this.adjacentProteinDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
- // }
- // for (const disorder of response.disorders) {
- // disorder.group = 'defaultDisorder';
- // disorder.id = disorder.drugstoneId;
- // this.adjacentProteinDisorderList.push(mapCustomNode(disorder, this.myConfig))
- // }
- // this.saveAddNodes(this.adjacentProteinDisorderList);
- // this.nodeData.edges.add(this.adjacentProteinDisorderEdgesList);
- // this.emitVisibleItems(true);
- // });
- // this.legendContext = this.adjacentDrugs ? 'adjacentDrugsAndDisorders' : 'adjacentDisorders';
- // } else {
- // this.saveRemoveDisorders(this.adjacentProteinDisorderList);
- // this.nodeData.edges.remove(this.adjacentProteinDisorderEdgesList);
- // this.adjacentProteinDisorderList = [];
- // this.adjacentProteinDisorderEdgesList = [];
- // this.legendContext = this.adjacentDisordersDrug ? this.legendContext : this.adjacentDrugs ? 'adjacentDrugs' : 'explorer';
- // this.emitVisibleItems(true);
- // }
- // }
-
- // public updateAdjacentDrugDisorders(bool: boolean) {
- // this.adjacentDisordersDrug = bool;
- // if (this.adjacentDisordersDrug) {
- // this.netex.adjacentDisorders(this.nodeData.nodes, 'drugs').subscribe(response => {
- // for (const interaction of response.edges) {
- // const edge = {from: interaction.drug, to: interaction.disorder};
- // this.adjacentDrugDisorderEdgesList.push(mapCustomEdge(edge, this.myConfig));
- // }
- // for (const disorder of response.disorders) {
- // disorder.group = 'defaultDisorder';
- // disorder.id = disorder.drugstoneId;
- // this.adjacentDrugDisorderList.push(mapCustomNode(disorder, this.myConfig));
- // }
- // this.saveAddNodes(this.adjacentDrugDisorderList);
- // this.nodeData.edges.add(this.adjacentDrugDisorderEdgesList);
- // this.emitVisibleItems(true);
- // });
- // this.legendContext = this.adjacentDrugs ? 'adjacentDrugsAndDisorders' : 'adjacentDisorders';
- // } else {
- // this.saveRemoveDisorders(this.adjacentDrugDisorderList);
- // this.nodeData.edges.remove(this.adjacentDrugDisorderEdgesList);
- // this.adjacentDrugDisorderList = [];
- // this.adjacentDrugDisorderEdgesList = [];
- // this.legendContext = this.adjacentDisordersProtein ? this.legendContext : this.adjacentDrugs ? 'adjacentDrugs' : 'explorer';
- // this.emitVisibleItems(true);
- // }
- // }
-
public downloadLink(view: string): string {
return `${environment.backend}task_result/?token=${this.token}&view=${view}&fmt=csv`;
}
- public inferEdgeGroup(edge: object): EdgeType {
- if (edge['to'].startsWith('d')) {
- return 'protein-drug';
- }
- return 'protein-protein';
- }
-
- /**
- * Infers wrapper type of node returned from backend.
- * Node can only be either an input node from the user with a defined group,
- * a drug found in the backend with either user defined type or default drug group,
- * or an intermediate protein added by the shortest path to the found drug.
- * For the third case, fall back to a default case which can also be set by user.
- */
- public inferNodeGroup(wrapper: Wrapper): string {
- if (wrapper.data.group !== undefined) {
- return wrapper.data.group;
- } else if (wrapper.data.drugstoneId !== undefined && wrapper.data.drugstoneId.startsWith('d')) {
- return 'drug';
- } else if (wrapper.data.drugstoneId !== undefined && wrapper.data.drugstoneId.startsWith('p')) {
- return 'protein';
- }
- }
-
- public inferNodeLabel(config: IConfig, wrapper: Wrapper): string {
- if (wrapper.data.label) {
- return wrapper.data.label;
- }
- const identifier = config.identifier;
- if (identifier === 'uniprot') {
- return wrapper.data.uniprotAc;
- } else if (identifier === 'symbol') {
- return wrapper.data.symbol;
- } else if (identifier === 'ensg') {
- // heuristc to find most important ensg is to look for smallest id
- // parse ensg numbers to integers
- const ensg_numbers = wrapper.data.ensg.map(x => parseInt(x));
- // get index of smalles number
- const i = ensg_numbers.reduce((iMin, x, i, arr) => x < arr[iMin] ? i : iMin, 0);
- // return ensg-ID
- return wrapper.data.ensg[i];
- }
- }
-
/**
* Maps analysis result returned from database to valid Vis.js network input
*
@@ -554,14 +431,14 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
// convert id to netex Id if exists
const nodeDetails = details[node];
- nodeDetails.id = nodeDetails.id ? nodeDetails.id : nodeDetails.drugstoneId;
- if (nodeDetails.drugstoneId && nodeDetails.drugstoneId.startsWith('p')) {
+ nodeDetails.id = nodeDetails.id ? nodeDetails.id : (typeof nodeDetails.drugstoneId === 'string' ? nodeDetails.drugstoneId : nodeDetails.drugstoneId[0]);
+ if (nodeDetails.drugstoneId && nodeDetails.drugstoneType === 'protein') {
// node is protein from database, has been mapped on init to backend protein from backend
// or was found during analysis
nodeDetails.group = nodeDetails.group ? nodeDetails.group : 'foundNode';
nodeDetails.label = nodeDetails.label ? nodeDetails.label : nodeDetails[identifier];
this.proteins.push(nodeDetails);
- } else if (nodeDetails.drugstoneId && nodeDetails.drugstoneId.startsWith('d')) {
+ } else if (nodeDetails.drugstoneId && nodeDetails.drugstoneType === 'drug') {
// node is drug, was found during analysis
nodeDetails.type = 'Drug';
nodeDetails.group = 'foundDrug';
@@ -583,72 +460,6 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
};
}
- // hasDrugsLoaded(): boolean {
- // if (this.nodeData == null || this.nodeData.nodes == null)
- // return false;
- // return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.drugstoneId.startsWith('dr')).length > 0;
- // }
-
- // public updateAdjacentDrugs(bool: boolean) {
- // this.adjacentDrugs = bool;
- // if (this.adjacentDrugs) {
- // this.netex.adjacentDrugs(this.myConfig.interactionDrugProtein, this.nodeData.nodes).subscribe(response => {
- // for (const interaction of response.pdis) {
- // const edge = {from: interaction.protein, to: interaction.drug};
- // this.adjacentDrugEdgesList.push(mapCustomEdge(edge, this.myConfig));
- // }
- // for (const drug of response.drugs) {
- // drug.group = 'foundDrug';
- // drug.id = getDrugNodeId(drug)
- // this.adjacentDrugList.push(mapCustomNode(drug, this.myConfig))
- // }
- // this.nodeData.nodes.add(this.adjacentDrugList);
- // this.nodeData.edges.add(this.adjacentDrugEdgesList);
- // this.emitVisibleItems(true);
- // })
- // this.legendContext = this.adjacentDisordersDrug || this.adjacentDisordersProtein ? 'adjacentDrugsAndDisorders' : 'adjacentDrugs';
- // } else {
- // this.nodeData.nodes.remove(this.adjacentDrugList);
- // this.nodeData.edges.remove(this.adjacentDrugEdgesList);
- // this.adjacentDrugList = [];
- // this.adjacentDrugEdgesList = [];
-
- // this.legendContext = this.adjacentDisordersDrug || this.adjacentDisordersProtein ? 'adjacentDisorders' : 'explorer';
- // this.emitVisibleItems(true);
- // }
- // }
-
- // public updatePhysicsEnabled(bool: boolean) {
- // this.drugstoneConfig.config.physicsOn = bool;
- // this.networkHandler.activeNetwork.networkInternal.setOptions({
- // physics: {
- // enabled: this.drugstoneConfig.config.physicsOn,
- // stabilization: {
- // enabled: false,
- // },
- // }
- // });
- // }
-
- // public toImage() {
- // this.downloadDom(this.networkWithLegendEl.nativeElement).catch(error => {
- // console.error("Falling back to network only screenshot. Some components seem to be inaccessable, most likely the legend is a custom image with CORS access problems on the host server side.")
- // this.downloadDom(this.networkHandler.activeNetwork.networkEl.nativeElement).catch(e => {
- // console.error("Some network content seems to be inaccessable for saving as a screenshot. This can happen due to custom images used as nodes. Please ensure correct CORS accessability on the images host server.")
- // console.error(e)
- // });
- // });
- // }
-
- // public downloadDom(dom: object) {
- // return domtoimage.toPng(dom, {bgcolor: '#ffffff'}).then((generatedImage) => {
- // const a = document.createElement('a');
- // a.href = generatedImage;
- // a.download = `Network.png`;
- // a.click();
- // });
- // }
-
public tableProteinSelection = (e): void => {
const oldSelection = [...this.tableSelectedProteins];
this.tableSelectedProteins = e;
@@ -669,93 +480,4 @@ export class AnalysisPanelComponent implements OnInit, OnChanges, AfterViewInit
this.analysis.addItems(addItems);
this.analysis.removeItems(removeItems);
}
-
- public previewStringArray(arr: string[], count: number): string {
- if (arr.length < count) {
- return arr.join(', ');
- } else {
- return arr.slice(0, count).join(', ') + `, ... (${arr.length})`;
- }
- }
-
- // public selectTissue(tissue: Tissue | null) {
- // this.expressionExpanded = false;
- // if (!tissue) {
- // this.selectedTissue = null;
- // const updatedNodes = [];
- // for (const item of this.proteins) {
- // if (item.drugstoneId === undefined) {
- // // nodes that are not mapped to backend remain untouched
- // continue;
- // }
- // const node: Node = this.nodeData.nodes.get(item.id);
- // if (!node) {
- // continue;
- // }
- // const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([item.id]);
- // node.x = pos[item.id].x;
- // node.y = pos[item.id].y;
- // const isSeed = this.highlightSeeds ? this.seedMap[node.id] : false;
- // Object.assign(
- // node,
- // NetworkSettings.getNodeStyle(
- // node,
- // this.myConfig,
- // isSeed,
- // this.analysis.inSelection(getWrapperFromNode(item)),
- // 1.0
- // )
- // )
- // updatedNodes.push(node);
- // }
- // this.nodeData.nodes.update(updatedNodes);
- // // delete expression values
- // this.expressionMap = undefined;
- // this.gradientMap = {};
- // } else {
- // this.selectedTissue = tissue
- // const minExp = 0.3;
- // // filter out non-proteins, e.g. drugs
- // const proteinNodes = [];
- // this.nodeData.nodes.forEach(element => {
- // if (element.id.startsWith('p') && element.drugstoneId !== undefined) {
- // proteinNodes.push(element);
- // }
- // });
- // this.netex.tissueExpressionGenes(this.selectedTissue, proteinNodes).subscribe((response) => {
- // this.expressionMap = response;
- // const updatedNodes = [];
- // // mapping from netex IDs to network IDs, TODO check if this step is necessary
- // const networkIdMappping = {}
- // this.nodeData.nodes.forEach(element => {
- // networkIdMappping[element.drugstoneId] = element.id
- // });
- // const maxExpr = Math.max(...Object.values(this.expressionMap));
- // for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
- // const networkId = networkIdMappping[drugstoneId]
- // const node = this.nodeData.nodes.get(networkId);
- // if (node === null) {
- // continue;
- // }
- // const wrapper = getWrapperFromNode(node)
- // this.gradientMap[drugstoneId] = expressionlvl !== null ? (Math.pow(expressionlvl / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
- // const pos = this.networkHandler.activeNetwork.networkInternal.getPositions([networkId]);
- // node.x = pos[networkId].x;
- // node.y = pos[networkId].y;
- // const isSeed = this.highlightSeeds ? this.seedMap[node.id] : false;
- // Object.assign(node,
- // NetworkSettings.getNodeStyle(
- // node,
- // this.myConfig,
- // isSeed,
- // this.analysis.inSelection(wrapper),
- // this.gradientMap[drugstoneId]));
- // node.shape = 'custom';
- // node.ctxRenderer = pieChartContextRenderer;
- // updatedNodes.push(node);
- // }
- // this.nodeData.nodes.update(updatedNodes);
- // })
- // }
- // }
}
diff --git a/src/app/components/info-tile/info-tile.component.html b/src/app/components/info-tile/info-tile.component.html
index dc8f22f3986e645db3a150e1550e54ca41cedc59..6b758796bb510463efac502f53edc5c1c17d38ae 100644
--- a/src/app/components/info-tile/info-tile.component.html
+++ b/src/app/components/info-tile/info-tile.component.html
@@ -71,10 +71,11 @@
<p *ngIf="wrapper.data.uniprotAc" [ngClass]="{ 'text-normal': drugstoneConfig.smallStyle }">
<b><span>Uniprot:</span></b>
<a
- href="https://www.uniprot.org/uniprot/{{ wrapper.data.uniprotAc }}"
+ *ngFor="let uniprotAc of wrapper.data.uniprotAc"
+ href="https://www.uniprot.org/uniprot/{{ uniprotAc }}"
target="_blank"
>
- <span class="is-capitalized"> {{ wrapper.data.uniprotAc }}</span>
+ <span class="is-capitalized"> {{ uniprotAc }}</span>
</a>
</p>
<p *ngIf="wrapper.data.ensg" [ngClass]="{ 'text-normal': drugstoneConfig.smallStyle }">
@@ -86,6 +87,16 @@
>
<span class="is-capitalized"> {{ ensg }}</span>
</a>
+ </p>
+ <p *ngIf="wrapper.data.entrez" [ngClass]="{ 'text-normal': drugstoneConfig.smallStyle }">
+ <b><span>Entrez:</span></b>
+ <a
+ *ngFor="let entrez of wrapper.data.entrez"
+ href="https://www.ncbi.nlm.nih.gov/gene/{{ entrez }}"
+ target="_blank"
+ >
+ <span class="is-capitalized"> {{ entrez }}</span>
+ </a>
</p>
<p *ngIf="wrapper.expression" [ngClass]="{ 'text-normal': drugstoneConfig.smallStyle }">
<b><span>Expression:</span></b>
@@ -98,10 +109,11 @@
><i class="fas fa-info-circle"></i
></span>
</p>
+
</div>
<app-toggle
- *ngIf="wrapper.data.drugstoneId && wrapper.data.drugstoneId.startsWith('p')"
+ *ngIf="wrapper.data.drugstoneId && wrapper.data.drugstoneType ==='protein'"
[value]="analysis.inSelection(wrapper)"
(valueChange)="
$event ? analysis.addItems([wrapper]) : analysis.removeItems([wrapper])
diff --git a/src/app/components/network/network.component.ts b/src/app/components/network/network.component.ts
index 442831fd3552595f5dfc588c26f2775c6ceb24f5..66638f719780b6732ea9d558e58809d11a0e85ae 100644
--- a/src/app/components/network/network.component.ts
+++ b/src/app/components/network/network.component.ts
@@ -101,7 +101,6 @@ export class NetworkComponent implements OnInit {
this.currentViewNodes.forEach((protein) => {
this.queryItems.push(getWrapperFromNode(protein));
});
- console.log(this.queryItems)
}
public saveAddNodes(nodeList: Node[]) {
@@ -113,10 +112,26 @@ export class NetworkComponent implements OnInit {
public updateAdjacentProteinDisorders(bool: boolean) {
this.adjacentDisordersProtein = bool;
if (this.adjacentDisordersProtein) {
- this.netex.adjacentDisorders(this.nodeData.nodes, 'proteins', this.drugstoneConfig.config.associatedProteinDisorder).subscribe(response => {
+
+ this.netex.adjacentDisorders(this.nodeData.nodes.get(), 'proteins', this.drugstoneConfig.config.associatedProteinDisorder, this.drugstoneConfig.config.licencedDatasets).subscribe(response => {
+ const proteinMap = this.getProteinMap()
+ const addedEdge = {}
for (const interaction of response.edges) {
- const edge = {from: interaction.protein, to: interaction.disorder};
- this.adjacentProteinDisorderEdgesList.push(mapCustomEdge(edge, this.drugstoneConfig.config));
+ const edge = mapCustomEdge({from: interaction.protein, to: interaction.disorder}, this.drugstoneConfig.config)
+
+ if (edge.from[0] === 'p')
+ edge.from = proteinMap[edge.from]
+ if (edge.to[0] === 'p')
+ edge.to = proteinMap[edge.to]
+ if (addedEdge[edge.to] && addedEdge[edge.to].indexOf(edge.from) !== -1)
+ continue
+ if (addedEdge[edge.from] && addedEdge[edge.from].indexOf(edge.to) !== -1)
+ continue
+ if (!addedEdge[edge.to])
+ addedEdge[edge.to] = [edge.from]
+ else
+ addedEdge[edge.to].push(edge.from)
+ this.adjacentProteinDisorderEdgesList.push(edge);
}
for (const disorder of response.disorders) {
disorder.group = 'defaultDisorder';
@@ -141,7 +156,7 @@ export class NetworkComponent implements OnInit {
public updateAdjacentDrugDisorders(bool: boolean) {
this.adjacentDisordersDrug = bool;
if (this.adjacentDisordersDrug) {
- this.netex.adjacentDisorders(this.nodeData.nodes, 'drugs', this.drugstoneConfig.config.indicationDrugDisorder).subscribe(response => {
+ this.netex.adjacentDisorders(this.nodeData.nodes.get(), 'drugs', this.drugstoneConfig.config.indicationDrugDisorder, this.drugstoneConfig.config.licencedDatasets).subscribe(response => {
for (const interaction of response.edges) {
const edge = {from: interaction.drug, to: interaction.disorder};
this.adjacentDrugDisorderEdgesList.push(mapCustomEdge(edge, this.drugstoneConfig.config));
@@ -166,15 +181,32 @@ export class NetworkComponent implements OnInit {
}
}
+ public getProteinMap() {
+ const proteinMap = {}
+ this.nodeData.nodes.get().forEach(n => {
+ if (n.drugstoneType === 'protein') {
+ n.drugstoneId.forEach(id => {
+ proteinMap[id] = n.id;
+ });
+ }
+ });
+ return proteinMap
+ }
+
public updateAdjacentDrugs(bool: boolean) {
this.adjacentDrugs = bool;
if (this.adjacentDrugs) {
- // console.log(this.nodeData.nodes)
- this.netex.adjacentDrugs(this.drugstoneConfig.config.interactionDrugProtein, this.nodeData.nodes).subscribe(response => {
- const existingDrugIDs = this.nodeData.nodes.get().filter(n => n.drugstoneId).map(n => n.drugstoneId);
+ const proteinMap = this.getProteinMap()
+ this.netex.adjacentDrugs(this.drugstoneConfig.config.interactionDrugProtein, this.drugstoneConfig.config.licencedDatasets, this.nodeData.nodes.get()).subscribe(response => {
+ const existingDrugIDs = this.nodeData.nodes.get().filter(n => n.drugstoneId && n.drugstoneType === 'drug').map(n => n.drugstoneId);
for (const interaction of response.pdis) {
- const edge = {from: interaction.protein, to: interaction.drug};
- this.adjacentDrugEdgesList.push(mapCustomEdge(edge, this.drugstoneConfig.config));
+ let edge = mapCustomEdge({from: interaction.protein, to: interaction.drug}, this.drugstoneConfig.config)
+ if (edge.from[0] === 'p')
+ edge.from = proteinMap[edge.from]
+ if (edge.to[0] === 'p')
+ edge.to = proteinMap[edge.to]
+
+ this.adjacentDrugEdgesList.push(edge);
}
for (const drug of response.drugs) {
drug.group = 'foundDrug';
@@ -309,53 +341,68 @@ export class NetworkComponent implements OnInit {
// filter out non-proteins, e.g. drugs
const proteinNodes = [];
this.nodeData.nodes.forEach(element => {
- if (element.id.startsWith('p') && element.drugstoneId !== undefined) {
+ if (element.drugstoneType === 'protein') {
proteinNodes.push(element);
}
});
this.netex.tissueExpressionGenes(this.selectedTissue, proteinNodes).subscribe((response) => {
- this.expressionMap = response;
- const updatedNodes = [];
- // mapping from netex IDs to network IDs, TODO check if this step is necessary
- const networkIdMappping = {}
- this.nodeData.nodes.forEach(element => {
- networkIdMappping[element.drugstoneId] = element.id
- });
- const maxExpr = Math.max(...Object.values(this.expressionMap));
- for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
- const networkId = networkIdMappping[drugstoneId]
- const node = this.nodeData.nodes.get(networkId);
- if (node === null) {
- continue;
+ this.expressionMap = response;
+ const updatedNodes = [];
+ // mapping from netex IDs to network IDs, TODO check if this step is necessary
+ const networkIdMappping = {}
+ this.nodeData.nodes.get().forEach(element => {
+ if (element.drugstoneType === 'protein') {
+ element.drugstoneId.forEach(id => {
+ networkIdMappping[id] = element.id;
+ });
+ }
+ });
+ const maxExpr = Math.max(...Object.values(this.expressionMap));
+ const exprMap = {}
+ for (const [drugstoneId, expressionlvl] of Object.entries(this.expressionMap)) {
+ const networkId = networkIdMappping[drugstoneId]
+ if (!exprMap[networkId])
+ exprMap[networkId] = [expressionlvl]
+ else
+ exprMap[networkId].push(expressionlvl)
}
- const wrapper = getWrapperFromNode(node)
- const gradient = expressionlvl !== null ? (Math.pow(expressionlvl / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
- const pos = this.networkInternal.getPositions([networkId]);
- node.x = pos[networkId].x;
- node.y = pos[networkId].y;
- Object.assign(node,
- NetworkSettings.getNodeStyle(
- node,
- this.drugstoneConfig.config,
- node.isSeed,
- this.analysis.inSelection(wrapper),
- gradient));
-
- // custom ctx renderer for pie chart
- node.shape = 'custom';
- node.ctxRenderer = pieChartContextRenderer;
- updatedNodes.push(node);
+ this.expressionMap = {}
+ Object.keys(exprMap).forEach(networkId => {
+ const expressionlvl = exprMap[networkId] ? exprMap[networkId].reduce((a, b) => a + b) / exprMap[networkId].length : null;
+ this.expressionMap[networkId] = expressionlvl
+ const node = this.nodeData.nodes.get(networkId);
+ if (node === null) {
+ return;
+ }
+ const wrapper = getWrapperFromNode(node);
+ const gradient = expressionlvl !== null ? (Math.pow(expressionlvl / maxExpr, 1 / 3) * (1 - minExp) + minExp) : -1;
+ const pos = this.networkInternal.getPositions([networkId]);
+ node.x = pos[networkId].x;
+ node.y = pos[networkId].y;
+ Object.assign(node,
+ NetworkSettings.getNodeStyle(
+ node,
+ this.drugstoneConfig.config,
+ node.isSeed,
+ this.analysis.inSelection(wrapper),
+ gradient));
+ // custom ctx renderer for pie chart
+ node.shape = 'custom';
+ node.ctxRenderer = pieChartContextRenderer;
+ updatedNodes.push(node);
+ })
+ this.nodeData.nodes.update(updatedNodes);
}
- this.nodeData.nodes.update(updatedNodes);
- })
+ )
}
+
this.currentViewSelectedTissue = this.selectedTissue;
}
public hasDrugsLoaded(): boolean {
if (this.nodeData == null || this.nodeData.nodes == null)
return false;
- return this.nodeData.nodes.get().filter((node: Node) => node.drugId && node.drugstoneId.startsWith('dr')).length > 0;
+ return this.nodeData.nodes.get().filter((node: Node) => node.drugId).map(node => node.drugstoneId).filter(id => id.startsWith('dr')).length > 0;
}
public setLegendContext() {
diff --git a/src/app/components/query-tile/query-tile.component.ts b/src/app/components/query-tile/query-tile.component.ts
index 0b1e6fe082a99491dc2d1027f20ffe62ca34a691..70485c9f47f21719062932d4be846c4cd3a9e40d 100644
--- a/src/app/components/query-tile/query-tile.component.ts
+++ b/src/app/components/query-tile/query-tile.component.ts
@@ -1,7 +1,7 @@
-import { Component, Input, Output, EventEmitter, OnInit, ViewChild } from '@angular/core';
-import { NgSelectComponent } from '@ng-select/ng-select';
-import { NetworkHandlerService } from 'src/app/services/network-handler/network-handler.service';
-import { Wrapper } from '../../interfaces';
+import {Component, Input, Output, EventEmitter, OnInit, ViewChild} from '@angular/core';
+import {NgSelectComponent} from '@ng-select/ng-select';
+import {NetworkHandlerService} from 'src/app/services/network-handler/network-handler.service';
+import {Wrapper} from '../../interfaces';
@Component({
selector: 'app-query-tile-component',
@@ -12,7 +12,7 @@ export class QueryTileComponent implements OnInit {
constructor(public networkHandler: NetworkHandlerService) {
- }
+ }
ngOnInit(): void {
this.networkHandler.getChange$.forEach(data => this.reset());
@@ -28,18 +28,13 @@ export class QueryTileComponent implements OnInit {
this.ngSelectComponent.handleClearClick();
}
- private listStartsWith = (elments: any[], term) => {
- for (const e of elments) {
- if (e.toLowerCase().indexOf(term) > -1) {
- return true;
- }
- }
- return false;
+ private entryInList = (elements: any[], term) => {
+ return elements.filter(s => s.toLowerCase().indexOf(term) !== -1).length > 0;
}
querySearch = (term: string, item: Wrapper) => {
term = term.toLowerCase();
- const data = { ...item.data }
+ const data = {...item.data}
// add possible missing attributes to not throw errors
if (data.ensg === undefined) {
data.ensg = []
@@ -51,20 +46,21 @@ export class QueryTileComponent implements OnInit {
data.type = ''
}
if (data.symbol === undefined) {
- data.symbol = ''
+ data.symbol = []
}
if (data.proteinName === undefined) {
- data.proteinName = ''
+ data.proteinName = []
}
if (data.uniprotAc === undefined) {
- data.uniprotAc = ''
+ data.uniprotAc = []
}
if (data.drugId === undefined) {
data.drugId = ''
}
- return data.symbol.toLowerCase().indexOf(term) > -1 || data.uniprotAc.toLowerCase().indexOf(term) > -1 ||
- data.label.toLowerCase().indexOf(term) > -1 || this.listStartsWith(data.ensg, term) || data.id.toLowerCase().indexOf(term) > -1
- || data.proteinName.toLowerCase().indexOf(term) > -1 || data.type.toLowerCase().indexOf(term) > -1 ||
+ const query = term.toLowerCase();
+ return this.entryInList(data.symbol, query) || this.entryInList(data.uniprotAc, query) ||
+ data.label.toLowerCase().indexOf(term) > -1 || this.entryInList(data.ensg, query) || data.id.toLowerCase().indexOf(term) > -1
+ || this.entryInList(data.proteinName, query) || data.type.toLowerCase().indexOf(term) > -1 ||
data.groupName.toLowerCase().indexOf(term) > -1 || data.drugId.toLowerCase().indexOf(term) > -1;
}
diff --git a/src/app/config.ts b/src/app/config.ts
index ab90b6039b04bbb8c4b0f6dbf788e41281015c17..ee9d639de7d92cc517817e78846ca64e170c701c 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -69,6 +69,7 @@ export interface IConfig {
interactionDrugProtein: InteractionDrugProteinDB;
interactionProteinProtein: InteractionProteinProteinDB;
indicationDrugDisorder: IndicationDrugDisorderDB;
+ licencedDatasets: boolean;
associatedProteinDisorder: AssociatedProteinDisorderDB;
autofillEdges: boolean;
interactions?: InteractionDatabase;
@@ -117,6 +118,7 @@ export const defaultConfig: IConfig = {
interactionProteinProtein: 'NeDRex',
associatedProteinDisorder: 'NeDRex',
indicationDrugDisorder: 'NeDRex',
+ licencedDatasets: false,
nodeShadow: true,
edgeShadow: true,
autofillEdges: true,
diff --git a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
index c1e8a59ceb88228e8a45a96243114f24b659b20a..e5f74c2e2bd10e0fab31cf4da841788eea252313 100644
--- a/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
+++ b/src/app/dialogs/add-expressed-proteins/add-expressed-proteins.component.ts
@@ -59,7 +59,7 @@ export class AddExpressedProteinsComponent implements OnChanges {
if (!this.currentViewProteins || this.expressionMap === undefined) {
return;
}
- this.proteins = this.currentViewProteins.filter(p => this.expressionMap[p.drugstoneId] >= threshold);
+ this.proteins = this.currentViewProteins.flatMap(p => p.drugstoneId).filter(p => this.expressionMap[p] >= threshold);
}
public close() {
diff --git a/src/app/dialogs/custom-proteins/custom-proteins.component.html b/src/app/dialogs/custom-proteins/custom-proteins.component.html
deleted file mode 100644
index 2b9cd9475920abb7ac73dc385c58702807b700ad..0000000000000000000000000000000000000000
--- a/src/app/dialogs/custom-proteins/custom-proteins.component.html
+++ /dev/null
@@ -1,69 +0,0 @@
-<div class="modal" [class.is-active]="show">
- <div class="modal-background"></div>
- <div class="modal-card">
- <header class="modal-card-head">
- <p class="modal-card-title">
- <span class="icon"><i class="fa fa-dna"></i></span>
- Add Custom Proteins
- </p>
- <button (click)="close()" class="delete" aria-label="close"></button>
- </header>
- <section class="modal-card-body">
- <div class="notification is-success" *ngIf="addedCount > 0">
- {{addedCount}} host proteins have been added to the selection.
- <div *ngIf="itemsFound.length > addedCount && !selectOnly">
- {{itemsFound.length - addedCount}} proteins have already been selected before.
- </div>
- <div *ngIf="itemsFound.length > addedCount && selectOnly">
- {{itemsFound.length - addedCount}} proteins either have been selected already or did not appear in the current graph.
- </div>
- </div>
- <div class="notification is-warning" *ngIf="itemsFound.length > 0 && addedCount === 0">
- <div *ngIf="itemsFound.length > addedCount && !selectOnly">
- {{itemsFound.length - addedCount}} proteins have already been selected before.
- </div>
- <div *ngIf="itemsFound.length > addedCount && selectOnly">
- {{itemsFound.length - addedCount}} proteins either have been selected already or did not appear in the current graph.
- </div>
- </div>
- <div class="notification is-danger" *ngIf="notFound.length > 0">
- The following {{notFound.length}} items could not be found and have been ignored:
- <ul><li class="not-found" *ngFor="let nf of notFound">{{nf}}</li></ul>
- </div>
- <div class="field">
- <label class="label" for="protein-list">List of items (Uniprot ids or Drugbank ids)</label>
- <div class="control">
- <textarea class="input" [ngModel]="textList" (ngModelChange)="changeTextList($event)" id="protein-list">
- </textarea>
- </div>
- </div>
- <p *ngIf="proteins">
- Items parsed: {{proteins.length}}
- </p>
- </section>
- <footer class="modal-card-foot">
- <button (click)="addProteins();" class="button is-success is-rounded has-tooltip"
- pTooltip="Add all to the selection." [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-top'" tooltipPosition="top"
- [disabled]="proteins.length === 0 || loading">
- <span class="icon">
- <i class="fa fa-plus"></i>
- </span>
- <span>
- Add
- </span>
- </button>
- <button (click)="addVisibleProteins();" class="button is-success is-rounded has-tooltip"
- pTooltip="Add to selection if they appear in the current network." [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-top'" tooltipPosition="top"
- [disabled]="proteins.length === 0 || loading">
- <span class="icon">
- <i class="fas fa-expand"></i>
- </span>
- <span>
- Select
- </span>
- </button>
- <button (click)="close()" class="button is-rounded has-tooltip" pTooltip="Close the current window." [tooltipStyleClass]="'drgstn drgstn-tooltip drgstn-tooltip-top'" tooltipPosition="top">Close
- </button>
- </footer>
- </div>
-</div>
diff --git a/src/app/dialogs/custom-proteins/custom-proteins.component.scss b/src/app/dialogs/custom-proteins/custom-proteins.component.scss
deleted file mode 100644
index a403b39782bc25c097682afc63824307d09520f1..0000000000000000000000000000000000000000
--- a/src/app/dialogs/custom-proteins/custom-proteins.component.scss
+++ /dev/null
@@ -1,10 +0,0 @@
-#protein-list {
- height: 150px;
-}
-
-.not-found {
- padding: 4px;
- margin: 4px;
- border-radius: 3px;
- background-color: rgba(255, 255, 255, 0.33);
-}
diff --git a/src/app/dialogs/custom-proteins/custom-proteins.component.ts b/src/app/dialogs/custom-proteins/custom-proteins.component.ts
deleted file mode 100644
index 3e94fc3223a905b084d4848377c9bf8eb2aaf701..0000000000000000000000000000000000000000
--- a/src/app/dialogs/custom-proteins/custom-proteins.component.ts
+++ /dev/null
@@ -1,110 +0,0 @@
-import {Component, EventEmitter, Input, OnInit, Output} from '@angular/core';
-import {HttpClient} from '@angular/common/http';
-import {environment} from '../../../environments/environment';
-import {getWrapperFromNode, Node, Wrapper} from '../../interfaces';
-import {AnalysisService} from '../../services/analysis/analysis.service';
-
-@Component({
- selector: 'app-custom-proteins',
- templateUrl: './custom-proteins.component.html',
- styleUrls: ['./custom-proteins.component.scss']
-})
-export class CustomProteinsComponent implements OnInit {
-
- @Input()
- public show = false;
- @Output()
- public showChange = new EventEmitter<boolean>();
- @Input()
- public visibleNodes: Array<any> = [];
-
- public textList = '';
- public proteins: Array<string> = [];
- public notFound: Array<string> = [];
- public itemsFound: Array<Wrapper> = [];
- public addedCount = 0;
- public selectOnly = false;
- public loading = false;
-
- constructor(private http: HttpClient, private analysis: AnalysisService) { }
-
- ngOnInit(): void {
- }
-
- public close() {
- this.show = false;
- this.textList = '';
- this.proteins = [];
- this.notFound = [];
- this.itemsFound = [];
- this.showChange.emit(this.show);
- this.addedCount = 0;
- this.selectOnly = false;
- }
-
- public async addProteins() {
- this.loading = true;
- this.notFound = [];
- this.itemsFound = [];
- const proteins = this.proteins;
- this.changeTextList('');
- const result = await this.http.post<any>(`${environment.backend}query_proteins/`, proteins).toPromise();
- this.notFound = result.notFound;
- const details = result.details;
- const items = [];
- for (const detail of details) {
- items.push(getWrapperFromNode(detail));
- }
- this.itemsFound = items;
- this.addedCount = this.analysis.addItems(items);
- this.selectOnly = false;
- this.loading = false;
- }
-
- public async addVisibleProteins() {
- this.loading = true;
- this.notFound = [];
- this.itemsFound = [];
- const proteins = this.proteins;
- this.changeTextList('');
- const result = await this.http.post<any>(`${environment.backend}query_proteins/`, proteins).toPromise();
- this.notFound = result.notFound;
- const details = result.details;
- const proteinItems = [];
- const items = [];
- for (const detail of details) {
- proteinItems.push(detail as Node);
- items.push(getWrapperFromNode(detail));
- }
- this.itemsFound = items;
- // this.addedCount = this.analysis.addVisibleHostProteins(this.visibleNodes, proteinItems);
- this.selectOnly = true;
- this.loading = false;
- }
-
- public changeTextList(textList) {
- this.textList = textList;
- if (!textList) {
- this.proteins = [];
- return;
- }
-
- const separators = ['\n', ',', ';', ' '];
-
- let proteins;
- for (const sep of separators) {
- if (textList.indexOf(sep) === -1) {
- continue;
- }
- proteins = textList.split(sep).map(ac => ac.trim()).filter(ac => !!ac);
- break;
- }
-
- if (!proteins) {
- proteins = [textList];
- }
-
- this.proteins = proteins;
- }
-
-}
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index 51dc79c8923579b41bbec7a762a5052305ac67a3..6a735f05a3b42adb23dea03f20d2a680212abee5 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -116,6 +116,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
};
parameters.ppi_dataset = this.config.interactionProteinProtein;
parameters.pdi_dataset = this.config.interactionDrugProtein;
+ parameters.licenced = this.config.licencedDatasets;
parameters.target = this.target === 'drug' ? 'drug' : 'drug-target';
// pass network data to reconstruct network in analysis result to connect non-proteins to results
// drop interactions in nodes beforehand to no cause cyclic error, information is contained in edges
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 59daa8bf3c2288312d232a032a9c018e5d70177c..35b259d7feca771ed0d4675a2ba2098e4132996b 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -2,16 +2,18 @@ import {AlgorithmType, QuickAlgorithmType} from './services/analysis/analysis.se
export interface Node {
label: string;
- symbol: string;
+ symbol: Array<string>;
id: string;
type: string;
- drugstoneId?: string;
- drugId?:string;
- uniprotAc?: string;
+ drugstoneId?: Array<string> | string;
+ drugstoneType: NodeType;
+ drugId?: string;
+ uniprotAc?: Array<string>;
ensg?: Array<string>;
+ entrez?: Array<string>;
group?: string;
groupName?: string;
- proteinName?: string;
+ proteinName?: Array<string>;
color?: string | any; // mostly any, but vis js allows detail settings
shape?: string;
image?: string;
@@ -37,10 +39,12 @@ export interface NodeData {
edges: any;
}
+export type NodeType= 'protein' | 'drug' | 'disorder' | 'other'
+
export type NetworkType = 'explorer' | 'analysis'
export type LegendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget' |
-'drugTargetAndSeeds' | 'drugAndSeeds' | 'adjacentDisorders' | 'adjacentDrugsAndDisorders';
+ 'drugTargetAndSeeds' | 'drugAndSeeds' | 'adjacentDisorders' | 'adjacentDrugsAndDisorders';
/// drugstoneId to expressionlvl
export type NodeAttributeMap = { string: number } | {};
@@ -181,16 +185,18 @@ export interface Wrapper {
id: string;
label: string;
type?: string;
- symbol?: string;
- drugstoneId?: string;
+ symbol?: Array<string>;
+ drugstoneId?: Array<string> |string;
+ drugstoneType: NodeType,
ensg?: Array<string>;
+ entrez?: Array<string>;
shape?: string;
color?: string;
interactions?: any;
group?: string;
groupName?: string;
- proteinName?: string;
- uniprotAc?: string;
+ proteinName?: Array<string>;
+ uniprotAc?: Array<string>;
expressionLevel?: number;
gradient?: number;
x?: number;
diff --git a/src/app/main-network.ts b/src/app/main-network.ts
index d00b176931e53eef6379ceebe57f723a10c1b67e..1917d22a363e5f4f06c845b154420fe8bc0f20ca 100644
--- a/src/app/main-network.ts
+++ b/src/app/main-network.ts
@@ -1,4 +1,4 @@
-import { defaultConfig, IConfig } from './config';
+import {defaultConfig, IConfig} from './config';
import {NodeInteraction, Node, getProteinNodeId, NetexInteraction} from './interfaces';
import * as merge from 'lodash/fp/merge';
@@ -64,14 +64,14 @@ export class ProteinNetwork {
}
/** Maps user input node to network node object
- * If user input node has no group, fall back to default
- * If user input node has group that is not defined, throw error
- *
- * @param customNode
- * @param config
- * @returns
- */
- export function mapCustomNode(customNode: any, config: IConfig): Node {
+ * If user input node has no group, fall back to default
+ * If user input node has group that is not defined, throw error
+ *
+ * @param customNode
+ * @param config
+ * @returns
+ */
+export function mapCustomNode(customNode: any, config: IConfig): Node {
let node;
if (customNode.group === undefined) {
// fallback to default node
@@ -125,10 +125,10 @@ export function mapCustomEdge(customEdge: NodeInteraction, config: IConfig): any
* @param config
* @returns
*/
- export function mapNetexEdge(customEdge: NetexInteraction, config: IConfig): any {
+export function mapNetexEdge(customEdge: NetexInteraction, config: IConfig, node_map: object): any {
const edge = JSON.parse(JSON.stringify(config.edgeGroups.default));
- edge['from'] = customEdge['proteinA'];
- edge['to'] = customEdge['proteinB'];
+ edge['from'] = node_map[customEdge['proteinA']];
+ edge['to'] = node_map[customEdge['proteinB']];
edge['dataset'] = customEdge['dataset'];
return edge;
}
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index 2d517d1c697a75822a005b8f6c773e71264c00f7..1922c4504bdcb398bd56721123ba776484bc9314 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -9,11 +9,6 @@
>
</app-launch-analysis>
- <app-custom-proteins
- [(show)]="showCustomProteinsDialog"
- [visibleNodes]="networkHandler.activeNetwork.currentViewNodes"
- >
- </app-custom-proteins>
<app-add-expressed-proteins
[(show)]="showThresholdDialog"
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index cf615e665f1d39e2c77a73dbc360f3b40f72689a..f3ea4ff961dfa6e5cce4c88f15da3e3a1b65e047 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -15,19 +15,19 @@ import {
Tissue,
Wrapper
} from '../../interfaces';
-import { ProteinNetwork, mapNetexEdge } from '../../main-network';
-import { AnalysisService } from '../../services/analysis/analysis.service';
-import { OmnipathControllerService } from '../../services/omnipath-controller/omnipath-controller.service';
-import { NetworkSettings } from '../../network-settings';
-import { defaultConfig, EdgeGroup, NodeGroup } from '../../config';
-import { NetexControllerService } from 'src/app/services/netex-controller/netex-controller.service';
-import { removeDuplicateObjectsFromList } from '../../utils';
+import {ProteinNetwork, mapNetexEdge} from '../../main-network';
+import {AnalysisService} from '../../services/analysis/analysis.service';
+import {OmnipathControllerService} from '../../services/omnipath-controller/omnipath-controller.service';
+import {NetworkSettings} from '../../network-settings';
+import {defaultConfig, EdgeGroup, NodeGroup} from '../../config';
+import {NetexControllerService} from 'src/app/services/netex-controller/netex-controller.service';
+import {removeDuplicateObjectsFromList} from '../../utils';
import * as merge from 'lodash/fp/merge';
-import { AnalysisPanelComponent } from 'src/app/components/analysis-panel/analysis-panel.component';
+import {AnalysisPanelComponent} from 'src/app/components/analysis-panel/analysis-panel.component';
import * as JSON5 from 'json5';
-import { DrugstoneConfigService } from 'src/app/services/drugstone-config/drugstone-config.service';
-import { NetworkHandlerService } from 'src/app/services/network-handler/network-handler.service';
-import { NetworkComponent } from 'src/app/components/network/network.component';
+import {DrugstoneConfigService} from 'src/app/services/drugstone-config/drugstone-config.service';
+import {NetworkHandlerService} from 'src/app/services/network-handler/network-handler.service';
+import {NetworkComponent} from 'src/app/components/network/network.component';
declare var vis: any;
@@ -96,7 +96,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
public edges: NodeInteraction[];
// this will store the vis Dataset
- public nodeData: { nodes: any, edges: any } = { nodes: null, edges: null };
+ public nodeData: { nodes: any, edges: any } = {nodes: null, edges: null};
public showAnalysisDialog = false;
public showThresholdDialog = false;
@@ -208,7 +208,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
}
}
// trigger updates on config e.g. in legend
- this.drugstoneConfig.config = { ...this.drugstoneConfig.config };
+ this.drugstoneConfig.config = {...this.drugstoneConfig.config};
if (updateNetworkFlag && typeof this.networkJSON !== 'undefined') {
// update network if network config has changed and networkJSON exists
if (this.networkHandler.activeNetwork.networkInternal !== null) {
@@ -251,17 +251,37 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.proteinData = new ProteinNetwork(this.proteins, this.edges);
if (this.networkHandler.activeNetwork.networkPositions) {
- this.proteinData.updateNodePositions(this.networkHandler.activeNetwork.networkPositions)
+ this.proteinData.updateNodePositions(this.networkHandler.activeNetwork.networkPositions);
}
- // TODO do we still need this?
- // this.proteinData.linkNodes();
-
- const { nodes, edges } = this.proteinData.mapDataToNetworkInput(this.drugstoneConfig.config);
+ let {nodes, edges} = this.proteinData.mapDataToNetworkInput(this.drugstoneConfig.config);
if (this.drugstoneConfig.config.autofillEdges && nodes.length) {
- const netexEdges = await this.netex.fetchEdges(nodes, this.drugstoneConfig.config.interactionProteinProtein);
- edges.push(...netexEdges.map(netexEdge => mapNetexEdge(netexEdge, this.drugstoneConfig.config)))
+ let node_map = {};
+ nodes.filter(n => n[this.drugstoneConfig.config.identifier]).forEach(node => {
+ if (typeof node.drugstoneId === 'string')
+ node_map[node.drugstoneId] = node.id;
+ else
+ node.drugstoneId.forEach(n => {
+ node_map[n] = node.id;
+ })
+ })
+ const netexEdges = await this.netex.fetchEdges(nodes, this.drugstoneConfig.config.interactionProteinProtein, this.drugstoneConfig.config.licencedDatasets);
+ edges.push(...netexEdges.map(netexEdge => mapNetexEdge(netexEdge, this.drugstoneConfig.config, node_map)));
}
+ const edge_map = {}
+
+ edges = edges.filter(edge => {
+ if (edge_map[edge.to] && edge_map[edge.to].indexOf(edge.from) !== -1)
+ return false
+ if (edge_map[edge.from] && edge_map[edge.from].indexOf(edge.to) !==-1)
+ return false
+ if(!edge_map[edge.from])
+ edge_map[edge.from] = [edge.to]
+ else
+ edge_map[edge.from].push(edge.to)
+ return true
+ })
+
this.nodeData.nodes = new vis.DataSet(nodes);
this.nodeData.edges = new vis.DataSet(edges);
const container = this.networkHandler.activeNetwork.networkEl.nativeElement;
@@ -275,7 +295,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (nodeIds != null && nodeIds.length > 0) {
const nodeId = nodeIds[0];
const node = this.nodeData.nodes.get(nodeId);
- if (node.drugstoneId === undefined || !node.drugstoneId.startsWith('p')) {
+ if (node.drugstoneId === undefined || node.drugstoneType !== 'protein') {
// skip if node is not a protein mapped to backend
return;
}
@@ -343,29 +363,24 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
network.nodes = await this.netex.mapNodes(network.nodes, this.drugstoneConfig.config.identifier);
}
- if (this.drugstoneConfig.config.identifier === 'ensg') {
- // remove possible duplicate IDs
- network.nodes = removeDuplicateObjectsFromList(network.nodes, 'drugstoneId');
- }
+ // if (this.drugstoneConfig.config.identifier === 'ensg') {
+ // remove possible duplicate IDs
+ // network.nodes = removeDuplicateObjectsFromList(network.nodes, 'drugstoneId');
+ // }
// at this point, we have nodes synched with the backend
// use drugstoneIds where posssible, but use original id as node name if no label given
- const nodeIdMap = {};
+ // const nodeIdMap = {};
network.nodes.forEach((node) => {
// set node label to original id before node id will be set to netex id
node.label = node.label ? node.label : node.id;
- nodeIdMap[node.id] = node.drugstoneId ? node.drugstoneId : node.id;
- node.id = nodeIdMap[node.id];
});
// adjust edge labels accordingly and filter
const edges = new Array();
if (network.edges != null)
network.edges.forEach(edge => {
- edge.from = nodeIdMap[edge.from];
- edge.to = nodeIdMap[edge.to];
- // check if edges have endpoints
if (edge.from !== undefined && edge.to !== undefined) {
edges.push(edge);
}
@@ -399,7 +414,8 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.showDetails = false;
}
- removeEnsemblVersion(versionId: string): string {
+ removeEnsemblVersion(versionId: string):
+ string {
return versionId.startsWith('ENSG') ? versionId.split('.')[0] : versionId;
}
@@ -496,7 +512,7 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
gProfilerLink(): string {
// nodes in selection have drugstoneId
const queryString = this.analysis.getSelection()
- .filter(wrapper => wrapper.data.drugstoneId.startsWith('p'))
+ .filter(wrapper => wrapper.data.drugstoneType === 'protein')
.map(wrapper => wrapper.data.uniprotAc)
.join('%0A');
return 'http://biit.cs.ut.ee/gprofiler/gost?' +
@@ -520,11 +536,11 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.taskEvent.emit(eventObject);
}
- setInputNetwork(network: any) {
- if (network == null)
- this.inputNetwork = { nodes: this.proteins, edges: this.edges }
- else
- this.inputNetwork = network;
- }
+ // setInputNetwork(network: any) {
+ // if (network == null)
+ // this.inputNetwork = {nodes: this.proteins, edges: this.edges}
+ // else
+ // this.inputNetwork = network;
+ // }
}
diff --git a/src/app/services/analysis/analysis.service.ts b/src/app/services/analysis/analysis.service.ts
index 1de35ee6bea9db78ea6fb6ace15a702b6516df8f..8bd2fc31f60bddb8555183599600dc0ef390ce63 100644
--- a/src/app/services/analysis/analysis.service.ts
+++ b/src/app/services/analysis/analysis.service.ts
@@ -227,11 +227,11 @@ export class AnalysisService {
const params = {
ppi_dataset: config.interactionProteinProtein,
pdi_dataset: config.interactionDrugProtein,
+ licenced: config.licencedDatasets,
config: config,
input_network: network,
seeds: isSuper ? network.nodes.filter(n => n.drugstoneId && n.drugstoneId[0] === 'p').map(n => n.drugstoneId) : this.getSelection().map((i) => i.id),
};
- console.log(params)
const resp = await this.http.post<any>(`${environment.backend}task/`, {
algorithm: isSuper ? 'super' : 'quick',
target: 'drug',
@@ -310,7 +310,9 @@ export class AnalysisService {
startWatching() {
const watch = async () => {
- if (this.tokens.length > 0) {
+ const finished = JSON.parse(localStorage.getItem(this.tokensFinishedCookieKey));
+ const unfinished = this.tokens.filter(t => finished.indexOf(t) === -1);
+ if (unfinished.length > 0) {
const newtasks = await this.getTasks();
if (newtasks.length === 0)
return;
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index bfb08c8243cf4500ec505c8e7239fb8c859a9cc3..ffaae7af197978fc67840fc75799347480dd9408 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -14,12 +14,12 @@ export class NetexControllerService {
constructor(private http: HttpClient) {
}
- public async getTask(token): Promise<any> {
- /**
- * returns promise of task status
- */
- return this.http.get(`${environment.backend}task/?tokens=${token}`).toPromise();
- }
+ // public async getTask(token): Promise<any> {
+ // /**
+ // * returns promise of task status
+ // */
+ // return this.http.get(`${environment.backend}task/?tokens=${token}`).toPromise();
+ // }
public async getTasks(tokens): Promise<any> {
/**
@@ -35,38 +35,38 @@ export class NetexControllerService {
return this.http.get<any>(`${environment.backend}task_result/?token=${token}`).toPromise();
}
- public async getTaskResultDrug(token): Promise<any> {
- /**
- * returns promise of drug view of task result of COMPLETED task
- */
- return this.http.get<any>(`${environment.backend}task_result/?token=${token}&view=drugs`).toPromise();
- }
-
- public async getTaskResultGene(token): Promise<any> {
- /**
- * returns promise of gene view of task result of COMPLETED task
- */
- return this.http.get<any>(`${environment.backend}task_result/?token=${token}&view=genes`).toPromise();
- }
-
- public async getTaskResultCancerNode(token): Promise<any> {
- /**
- * returns promise of cancer driver gene view of task result of COMPLETED task
- */
- return this.http.get<any>(`${environment.backend}task_result/?token=${token}&view=cancer_driver_genes`).toPromise();
- }
-
- public async postTask(algorithm: QuickAlgorithmType | AlgorithmType, target, parameters,) {
- /**
- * sends a task to task service
- */
-
- return this.http.post<any>(`${environment.backend}task/`, {
- algorithm,
- target,
- parameters,
- }).toPromise();
- }
+ // public async getTaskResultDrug(token): Promise<any> {
+ // /**
+ // * returns promise of drug view of task result of COMPLETED task
+ // */
+ // return this.http.get<any>(`${environment.backend}task_result/?token=${token}&view=drugs`).toPromise();
+ // }
+
+ // public async getTaskResultGene(token): Promise<any> {
+ // /**
+ // * returns promise of gene view of task result of COMPLETED task
+ // */
+ // return this.http.get<any>(`${environment.backend}task_result/?token=${token}&view=genes`).toPromise();
+ // }
+
+ // public async getTaskResultCancerNode(token): Promise<any> {
+ // /**
+ // * returns promise of cancer driver gene view of task result of COMPLETED task
+ // */
+ // return this.http.get<any>(`${environment.backend}task_result/?token=${token}&view=cancer_driver_genes`).toPromise();
+ // }
+
+ // public async postTask(algorithm: QuickAlgorithmType | AlgorithmType, target, parameters,) {
+ // /**
+ // * sends a task to task service
+ // */
+ //
+ // return this.http.post<any>(`${environment.backend}task/`, {
+ // algorithm,
+ // target,
+ // parameters,
+ // }).toPromise();
+ // }
public async mapNodes(nodes, identifier): Promise<any> {
/**
@@ -89,35 +89,33 @@ export class NetexControllerService {
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
// slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
- const genesBackendIds = nodes.map((node: Node) => node.drugstoneId ? node.drugstoneId.slice(1) : undefined);
+ const genesBackendIds = nodes.flatMap((node: Node) => node.drugstoneId ? node.drugstoneId : []).map((id: string | undefined) => id ? id.slice(1) : undefined);
const params = new HttpParams()
.set('tissue', tissue.drugstoneId)
.set('proteins', JSON.stringify(genesBackendIds));
return this.http.get(`${environment.backend}tissue_expression/`, {params});
}
- public adjacentDisorders(nodes: Node[], nodeType: string, dataset: string): Observable<any> {
-
- const params = {dataset:dataset};
+ public adjacentDisorders(nodes: Node[], nodeType: string, dataset: string, licenced: boolean): Observable<any> {
+ const params = {dataset: dataset, licenced: licenced};
if (nodeType === 'proteins') {
- // @ts-ignore
- params.proteins = nodes.map((node: Node) => node.drugstoneId && node.drugstoneId.startsWith('p') ? node.drugstoneId.slice(1) : undefined).filter(id => id != null);
+ params["proteins"] = nodes.filter((node: Node) => node.drugstoneId && node.drugstoneType === 'protein').flatMap((node: Node) => node.drugstoneId).map(id => id.slice(1));
} else if (nodeType === 'drugs') {
- // @ts-ignore
- params.drugs = nodes.map((node: Node) => node.drugId && node.drugstoneId.startsWith('dr') ? node.drugstoneId.slice(2) : undefined).filter(id => id != null);
+ params["drugs"] = nodes.map((node: Node) => node.drugId && node.drugstoneType === 'drug' ? node.drugstoneId.slice(2) : undefined).filter(id => id != null);
}
return this.http.post<any>(`${environment.backend}adjacent_disorders/`, params);
}
- public adjacentDrugs(pdiDataset: InteractionDrugProteinDB, nodes: Node[]): Observable<any> {
+ public adjacentDrugs(pdiDataset: InteractionDrugProteinDB, licenced: boolean, nodes: Node[]): Observable<any> {
/**
* Returns the expression in the given tissue for given nodes and cancerNodes
*/
// slice prefix of netex id away for direct lookup in db, if node not mapped to db, replace by undefined
- const genesBackendIds = nodes.map((node: Node) => node.drugstoneId && node.drugstoneId.startsWith('p') ? node.drugstoneId.slice(1) : undefined).filter(id => id != null);
+ const genesBackendIds = nodes.filter((node: Node) => node.drugstoneId && node.drugstoneType === 'protein').flatMap(node => node.drugstoneId).map(id => id.slice(1));
const params = {
pdi_dataset: pdiDataset,
- proteins: genesBackendIds
+ proteins: genesBackendIds,
+ licenced: licenced
};
return this.http.post<any>(`${environment.backend}adjacent_drugs/`, params);
}
@@ -130,12 +128,12 @@ export class NetexControllerService {
return this.http.post(`${environment.backend}graph_export/`, graph_data, {responseType: 'text'});
}
- public async fetchEdges(nodes: Node[], dataset: InteractionProteinProteinDB): Promise<any> {
+ public async fetchEdges(nodes: Node[], dataset: InteractionProteinProteinDB, licenced: boolean): Promise<any> {
/**
* Tries to map every node to a node object in out database
* Returns list of mapped nodes if node was found, otherwise original node to not lose information
*/
- const payload = {nodes: nodes, dataset: dataset};
+ const payload = {nodes: nodes, dataset: dataset, licenced: licenced};
return this.http.post(`${environment.backend}fetch_edges/`, payload).toPromise();
}
}
diff --git a/src/index.html b/src/index.html
index 83d4eea9e49e108271b48470808e1cc52e1728fc..077915068496ff1acded1577f9512549863d9819 100644
--- a/src/index.html
+++ b/src/index.html
@@ -41,13 +41,14 @@
<br>
<br>
<b>Datasets</b>
+<input type="checkbox" onclick=changeLicenced(this.checked) /> Use licenced datasets<br>
<div>
<i>Protein-Protein Interactions</i>
<select name="Protein-Protein Interactions" onchange="applyDataset()" id="ppi-dataset">
<option value="STRING">STRING</option>
<option value="NeDRex">NeDRex</option>
- <option value="BioGRID">BioGRID</option>
- <option value="IID">IID</option>
+ <option value="biogrid">BioGRID</option>
+ <option value="iid">IID</option>
<option value="IntAct">IntAct</option>
<option value="APID">APID</option>
</select>
@@ -91,7 +92,7 @@
<drugst-one id="netexp1"
pluginId="2"
- config='{"interactionProteinProtein":"STRING","interactionDrugProtein":"NeDRex","indicationDrugDisorder":"NeDRex","associatedProteinDisorder":"NeDRex", "nodeGroups":{"patient":{"type":"patient","color":"#000000","font":{"color":"#000000"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"#000000","font":{"color":"#000000"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#f0f0f0"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":"#F12590","font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"#000000","groupName":"Relevant Gene"},"has-condition":{"color":"#000000","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":true,"showLegend":true}'
+ config='{"licencedDatasets": false, "interactionDrugProtein":"NeDRex", "physicsOn":true, "showLeftSidebar": true, "showSimpleAnalysis":true, "nodeGroups":{"patient":{"type":"patient","color":"black","font":{"color":"#ffffff"},"groupName":"Patient","shape":"image","image":"https://static.thenounproject.com/png/22780-200.png"},"condition":{"type":"condition","color":"black","font":{"color":"black"},"groupName":"Condition","shape":"text"},"important":{"type":"gene","color":"#ff881f","font":{"color":"#000000"},"groupName":"Important Gene","shape":"star"},"gene":{"type":"gene","color":"#4da300","font":{"color":"#ffffff"},"groupName":"Gene","shape":"circle"},"foundDrug":{"type":"drug","color":{"border":"#F12590","background":"#F12590"},"font":{"color":"#000000"},"groupName":"Drug","shape":"diamond"}},"edgeGroups":{"genotype":{"color":"black","groupName":"Relevant Gene"},"has-condition":{"color":"#ffffff","groupName":"Has Condition","dashes":[2,2]},"default":{"color":"#000000","groupName":"default edge"},"ggi":{"color":"#000000","groupName":"Interaction","dashes":[3,2]}},"identifier":"symbol","title":"Breast cancer example network","nodeShadow":true,"edgeShadow":false,"autofillEdges":true,"showLegend":true}'
network='{"nodes":[{"id":"patient-1","group":"patient","x":592,"y":446},{"id":"patient-2","group":"patient","x":235,"y":87},{"id":"patient-3","group":"patient","x":105,"y":369},{"id":"ATM","label":"ATM","group":"gene","x":289,"y":242},{"id":"BARD1","label":"BARD1","group":"gene","x":44,"y":250},{"id":"BRCA1","label":"BRCA1","group":"gene","x":466,"y":576},{"id":"BRCA2","label":"BRCA2","group":"gene","x":507,"y":285},{"id":"BRIP1","label":"BRIP1","group":"gene","x":54,"y":474},{"id":"CHEK2","label":"CHEK2","group":"gene","x":216,"y":590},{"id":"CDH1","label":"CDH1","group":"gene","x":320,"y":-57},{"id":"NF1","label":"NF1","group":"gene","x":481,"y":111},{"id":"NBN","label":"NBN","group":"gene","x":-57,"y":314},{"id":"PALB2","label":"PALB2","group":"gene","x":450,"y":190},{"id":"PTEN","label":"PTEN","group":"important","x":305,"y":494},{"id":"RAD51C","label":"RAD51C","group":"gene","x":182,"y":-90},{"id":"RAD51D","label":"RAD51D","group":"gene","x":368,"y":73},{"id":"STK11","label":"STK11","group":"gene","x":686,"y":330},{"id":"TP53","label":"TP53","group":"important","x":333,"y":316},{"id":"subtype-1","label":"Subtype 1","group":"condition","x":556,"y":171},{"id":"subtype-2","label":"Subtype 2","group":"condition","x":-87,"y":221}],"edges":[{"from":"patient-1","to":"BRCA1","group":"genotype"},{"from":"patient-1","to":"TP53","group":"genotype"},{"from":"patient-1","to":"BRCA2","group":"genotype"},{"from":"patient-1","to":"PTEN","group":"genotype"},{"from":"patient-2","to":"TP53","group":"genotype"},{"from":"patient-2","to":"NF1","group":"genotype"},{"from":"patient-2","to":"BARD1","group":"genotype"},{"from":"patient-3","to":"TP53","group":"genotype"},{"from":"patient-3","to":"PTEN","group":"genotype"},{"from":"patient-3","to":"NBN","group":"genotype"},{"from":"patient-1","to":"subtype-1","group":"has-condition"},{"from":"patient-2","to":"subtype-1","group":"has-condition"},{"from":"patient-3","to":"subtype-2","group":"has-condition"}]}'>
</drugst-one>
</div>
@@ -144,26 +145,31 @@
document.getElementsByTagName("network-expander")[0].addEventListener("taskEvent",(event)=>{console.log(event.detail)})
}
+ function changeLicenced(licenced){
+ setAttribute('licencedDatasets',licenced)
+
+ }
+
function applyDataset(){
let ppi = document.getElementById('ppi-dataset')
- setDataset('interactionProteinProtein',ppi.options[ppi.selectedIndex].value)
+ setAttribute('interactionProteinProtein',ppi.options[ppi.selectedIndex].value)
let drpi = document.getElementById('drpi-dataset')
- setDataset('interactionDrugProtein', drpi.options[drpi.selectedIndex].value)
+ setAttribute('interactionDrugProtein', drpi.options[drpi.selectedIndex].value)
let drdi = document.getElementById('drdi-dataset')
- setDataset('indicationDrugDisorder', drdi.options[drdi.selectedIndex].value)
+ setAttribute('indicationDrugDisorder', drdi.options[drdi.selectedIndex].value)
let pdis = document.getElementById('pdis-dataset')
- setDataset('associatedProteinDisorder', pdis.options[pdis.selectedIndex].value)
+ setAttribute('associatedProteinDisorder', pdis.options[pdis.selectedIndex].value)
}
- function setDataset(name, dataset){
+ function setAttribute(name, value){
// console.log(event)
- console.log("Dataset "+name+" -> "+dataset)
+ console.log("Attribute "+name+" -> "+value)
const netexp = document.getElementById('netexp1');
config = JSON.parse(netexp.getAttribute('config'))
console.log(config)
- config[name]=dataset
+ config[name]=value
changeConfigStr(JSON.stringify(config))
}
diff --git a/tsconfig.json b/tsconfig.json
index a409145307e732d6957c0ee3f5cbfd8cc79474b0..3f289dbd635402eb725ad805993a98ee9c975978 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -15,7 +15,7 @@
"node_modules/@types"
],
"lib": [
- "es2018",
+ "es2019",
"dom"
]
},