@sjcrh/proteinpaint-server 2.16.0 → 2.18.0

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Files changed (22) hide show
  1. package/dataset/clinvar.hg19.js +53 -51
  2. package/dataset/clinvar.hg38.js +60 -58
  3. package/dataset/clinvar.js +49 -55
  4. package/genome/CriGri.js +23 -1853
  5. package/genome/danRer10.js +48 -1108
  6. package/genome/dm3.js +47 -60
  7. package/genome/dm6.js +48 -1916
  8. package/genome/galGal5.js +48 -23522
  9. package/genome/galGal6.js +48 -512
  10. package/genome/hg19.js +210 -304
  11. package/genome/hg38.js +110 -474
  12. package/genome/hg38.test.js +42 -409
  13. package/genome/hgvirus.js +21 -43
  14. package/genome/mm10.js +70 -135
  15. package/genome/mm9.js +82 -118
  16. package/genome/rn6.js +49 -1000
  17. package/package.json +11 -7
  18. package/server.js +1 -1
  19. package/shared/common.js +4 -0
  20. package/src/serverconfig.js +10 -2
  21. package/utils/fastclust.R +16 -6
  22. package/genome/genome.sql +0 -54
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@sjcrh/proteinpaint-server",
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- "version": "2.16.0",
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+ "version": "2.18.0",
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  "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
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  "main": "server.js",
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  "bin": "start.js",
@@ -10,12 +10,13 @@
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  },
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  "scripts": {
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  "dev": "webpack --env NODE_ENV=development --watch --color",
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- "start": "nodemon --enable-source-maps server.js --watch ./server*.js* --watch genome --watch dataset",
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- "pretest": "./test/pretest.js",
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+ "start": "tsc --esModuleInterop genome/*.ts dataset/*.ts && nodemon --enable-source-maps server.js --watch ./server*.js* --watch dataset/*.ts --watch genome/*.ts",
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+ "pretest": "tsc --esModuleInterop genome/*.ts dataset/*.ts && ./test/pretest.js",
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  "test": "webpack --env NODE_ENV=test exportsFilename=all-test-context.js && node --enable-source-maps test/serverTests.js",
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- "test:unit": "webpack --env NODE_ENV=test exportsFilename=unit-test-context.js && node --enable-source-maps test/serverTests.js",
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+ "test:unit": "webpack --env NODE_ENV=test exportsFilename=unit-test-context.js && tsc --esModuleInterop dataset/*.ts && node --enable-source-maps test/serverTests.js",
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+ "pretest:integration": "tsc --esModuleInterop genome/*.ts dataset/*.ts",
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  "test:integration": "echo 'TODO: server integration tests'",
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- "prepack": "webpack --env NODE_ENV=production",
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+ "prepack": "tsc --esModuleInterop genome/*.ts dataset/*.ts && webpack --env NODE_ENV=production",
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  "response": "nodemon modules/test/test.server.js --watch src",
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  "getconf": "../build/getConfigProp.js"
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  },
@@ -26,12 +27,15 @@
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  "@babel/plugin-proposal-optional-chaining": "^7.9.0",
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  "@babel/plugin-transform-runtime": "^7.14.5",
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  "@babel/preset-env": "^7.9.6",
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+ "@babel/preset-typescript": "^7.21.4",
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  "@babel/register": "^7.14.5",
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  "babel-loader": "^8.2.2",
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  "node-watch": "^0.7.1",
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  "nodemon": "^2.0.19",
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- "prettier": "1.18.2",
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+ "prettier": "^2.8.8",
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  "tape": "^5.2.2",
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+ "typescript": "^5.0.3",
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+ "@typescript-eslint/eslint-plugin": "^5.60.0",
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  "webpack": "^5.76.0",
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  "webpack-cli": "^4.9.2",
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  "webpack-node-externals": "^3.0.0",
@@ -67,7 +71,7 @@
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  "bin.js",
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  "dataset/clinvar*.js",
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  "dataset/gdc*.js",
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- "genome",
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+ "genome/*.js",
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  "src/serverconfig.js",
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  "src/lines2R.js",
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  "src/mds3.gdc.filter.js",