@datagrok/sequence-translator 1.0.17 → 1.1.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (100) hide show
  1. package/.eslintrc.json +4 -3
  2. package/CHANGELOG.md +36 -0
  3. package/detectors.js +8 -0
  4. package/dist/package-test.js +2 -73079
  5. package/dist/package-test.js.map +1 -0
  6. package/dist/package.js +2 -72284
  7. package/dist/package.js.map +1 -0
  8. package/files/axolabs-style.json +97 -0
  9. package/files/codes-to-symbols.json +67 -0
  10. package/files/formats-to-helm.json +63 -0
  11. package/files/linkers.json +22 -0
  12. package/files/monomer-lib.json +1142 -0
  13. package/link-bio +7 -0
  14. package/package.json +30 -31
  15. package/scripts/build-monomer-lib.py +391 -122
  16. package/src/demo/demo-st-ui.ts +71 -0
  17. package/src/demo/handle-error.ts +12 -0
  18. package/src/model/axolabs/axolabs-tab.ts +111 -0
  19. package/src/model/axolabs/const.ts +33 -0
  20. package/src/{axolabs-tab → model/axolabs}/draw-svg.ts +1 -1
  21. package/src/{axolabs-tab → model/axolabs}/helpers.ts +7 -5
  22. package/src/model/const.ts +18 -0
  23. package/src/model/data-loading-utils/const.ts +8 -0
  24. package/src/model/data-loading-utils/json-loader.ts +38 -0
  25. package/src/model/data-loading-utils/types.ts +30 -0
  26. package/src/model/format-translation/const.ts +8 -0
  27. package/src/model/format-translation/conversion-utils.ts +49 -0
  28. package/src/model/format-translation/format-converter.ts +109 -0
  29. package/src/model/helpers.ts +12 -0
  30. package/src/model/monomer-lib/const.ts +3 -0
  31. package/src/model/monomer-lib/lib-wrapper.ts +119 -0
  32. package/src/model/parsing-validation/format-detector.ts +57 -0
  33. package/src/model/parsing-validation/sequence-validator.ts +52 -0
  34. package/src/model/sequence-to-structure-utils/const.ts +1 -0
  35. package/src/{utils/structures-works → model/sequence-to-structure-utils}/mol-transformations.ts +33 -41
  36. package/src/model/sequence-to-structure-utils/monomer-code-parser.ts +92 -0
  37. package/src/model/sequence-to-structure-utils/sdf-tab.ts +97 -0
  38. package/src/model/sequence-to-structure-utils/sequence-to-molfile.ts +409 -0
  39. package/src/package-test.ts +3 -1
  40. package/src/package.ts +113 -91
  41. package/src/tests/const.ts +24 -0
  42. package/src/tests/formats-support.ts +40 -0
  43. package/src/tests/formats-to-helm.ts +53 -0
  44. package/src/tests/helm-to-nucleotides.ts +28 -0
  45. package/src/view/const/main-tab.ts +3 -0
  46. package/src/view/const/view.ts +10 -0
  47. package/src/view/css/axolabs-tab.css +1 -0
  48. package/src/view/css/colored-text-input.css +27 -0
  49. package/src/view/css/main-tab.css +46 -0
  50. package/src/view/css/sdf-tab.css +39 -0
  51. package/src/view/monomer-lib-viewer/viewer.ts +22 -0
  52. package/src/view/tabs/axolabs.ts +719 -0
  53. package/src/view/tabs/main.ts +174 -0
  54. package/src/view/tabs/sdf.ts +193 -0
  55. package/src/view/utils/app-info-dialog.ts +18 -0
  56. package/src/view/utils/colored-input/colored-text-input.ts +56 -0
  57. package/src/view/utils/colored-input/input-painters.ts +44 -0
  58. package/src/view/utils/draw-molecule.ts +86 -0
  59. package/src/view/utils/molecule-img.ts +106 -0
  60. package/src/view/view.ts +127 -0
  61. package/tsconfig.json +12 -18
  62. package/webpack.config.js +17 -4
  63. package/README.md +0 -84
  64. package/css/style.css +0 -18
  65. package/img/Sequence Translator Axolabs.png +0 -0
  66. package/jest.config.js +0 -33
  67. package/setup-unlink-clean.cmd +0 -14
  68. package/setup-unlink-clean.sh +0 -21
  69. package/setup.cmd +0 -14
  70. package/setup.sh +0 -37
  71. package/src/__jest__/remote.test.ts +0 -77
  72. package/src/__jest__/test-node.ts +0 -97
  73. package/src/apps/oligo-sd-file-app.ts +0 -58
  74. package/src/autostart/calculations.ts +0 -40
  75. package/src/autostart/constants.ts +0 -37
  76. package/src/autostart/registration.ts +0 -306
  77. package/src/axolabs-tab/axolabs-tab.ts +0 -873
  78. package/src/axolabs-tab/define-pattern.ts +0 -874
  79. package/src/hardcode-to-be-eliminated/ICDs.ts +0 -3
  80. package/src/hardcode-to-be-eliminated/IDPs.ts +0 -3
  81. package/src/hardcode-to-be-eliminated/const.ts +0 -5
  82. package/src/hardcode-to-be-eliminated/constants.ts +0 -101
  83. package/src/hardcode-to-be-eliminated/converters.ts +0 -323
  84. package/src/hardcode-to-be-eliminated/map.ts +0 -720
  85. package/src/hardcode-to-be-eliminated/salts.ts +0 -2
  86. package/src/hardcode-to-be-eliminated/sources.ts +0 -3
  87. package/src/hardcode-to-be-eliminated/users.ts +0 -3
  88. package/src/main-tab/main-tab.ts +0 -210
  89. package/src/sdf-tab/sdf-tab.ts +0 -163
  90. package/src/sdf-tab/sequence-codes-tools.ts +0 -347
  91. package/src/tests/smiles-tests.ts +0 -458
  92. package/src/utils/const.ts +0 -0
  93. package/src/utils/helpers.ts +0 -28
  94. package/src/utils/parse.ts +0 -27
  95. package/src/utils/sdf-add-columns.ts +0 -118
  96. package/src/utils/sdf-save-table.ts +0 -56
  97. package/src/utils/structures-works/draw-molecule.ts +0 -84
  98. package/src/utils/structures-works/from-monomers.ts +0 -266
  99. package/test-SequenceTranslator-6288c2fbe346-695b7b55.html +0 -259
  100. package/vendors/openchemlib-full.js +0 -293
package/link-bio ADDED
@@ -0,0 +1,7 @@
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+ #!/bin/bash
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+
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+ cd ../../libraries/bio
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+ ./cleanup && npm i && npm run build && npm link
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+
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+ cd -
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+ npm link @datagrok-libraries/bio
package/package.json CHANGED
@@ -1,52 +1,47 @@
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  {
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  "name": "@datagrok/sequence-translator",
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  "friendlyName": "Sequence Translator",
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- "version": "1.0.17",
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+ "version": "1.1.4",
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  "author": {
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  "name": "Alexey Choposky",
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  "email": "achopovsky@datagrok.ai"
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  },
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- "description": "SequenceTranslator is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform, used to translate [oligonucleotide](https://en.wikipedia.org/wiki/Oligonucleotide) sequences between [different representations](https://github.com/datagrok-ai/public/tree/master/packages/SequenceTranslator#sequence-representations).",
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+ "description": "SequenceTranslator translates [oligonucleotide](https://en.wikipedia.org/wiki/Oligonucleotide) sequences between [different representations](https://github.com/datagrok-ai/public/tree/master/packages/SequenceTranslator#sequence-representations).",
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  "repository": {
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  "type": "git",
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  "url": "https://github.com/datagrok-ai/public.git",
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  "directory": "packages/SequenceTranslator"
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  },
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  "dependencies": {
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+ "@datagrok-libraries/bio": "^5.32.1",
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+ "@datagrok-libraries/chem-meta": "^1.0.9",
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+ "@datagrok-libraries/tutorials": "^1.3.2",
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  "@datagrok-libraries/utils": "^1.17.2",
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  "@types/react": "^18.0.15",
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- "@datagrok-libraries/bio": "^5.11.1",
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- "@deck.gl/core": "8.8.12",
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- "@luma.gl/core": "8.5.17",
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- "datagrok-api": "^1.8.2",
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- "datagrok-tools": "^4.1.2",
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- "npm": "^8.11.0",
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+ "cash-dom": "^8.1.0",
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+ "datagrok-api": "^1.15.2",
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  "openchemlib": "6.0.1",
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  "save-svg-as-png": "^1.4.17",
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  "ts-loader": "^9.3.1",
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  "typescript": "^4.7.4"
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  },
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  "devDependencies": {
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- "@types/jest": "^27.0.0",
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+ "@datagrok/bio": "^2.10.0",
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+ "@datagrok/chem": "1.7.2",
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  "@types/jquery": "^3.5.14",
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- "@typescript-eslint/eslint-plugin": "^4.29.1",
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- "@typescript-eslint/parser": "^4.29.1",
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- "cash-dom": "^8.1.0",
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- "eslint": "^7.32.0",
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- "eslint-config-google": "^0.14.0",
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- "jest": "^27.0.0",
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- "jest-html-reporter": "^3.5.0",
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- "puppeteer": "^13.7.0",
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- "ts-jest": "^27.0.0",
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- "webpack": "^5.31.0",
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- "webpack-cli": "^4.6.0",
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  "@types/js-yaml": "^4.0.5",
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- "js-yaml": "^4.1.0",
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  "@types/node-fetch": "^2.6.2",
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- "node-fetch": "^2.6.7"
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- },
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- "grokDependencies": {
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- "@datagrok/chem": "1.3.32"
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+ "@types/react": "^18.0.15",
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+ "@typescript-eslint/eslint-plugin": "latest",
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+ "@typescript-eslint/parser": "parser",
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+ "css-loader": "^6.7.3",
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+ "eslint": "^7.32.0",
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+ "eslint-config-google": "latest",
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+ "style-loader": "^3.3.1",
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+ "ts-loader": "^9.3.1",
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+ "typescript": "^4.7.4",
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+ "webpack": "^5.75.0",
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+ "webpack-cli": "latest"
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  },
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  "scripts": {
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  "link-api": "npm link datagrok-api",
@@ -59,13 +54,17 @@
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  "release-sequencetranslator-public": "grok publish public --release",
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  "debug-sequencetranslator-local": "grok publish local",
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  "release-sequencetranslator-local": "grok publish local --release",
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- "test": "jest",
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- "test-dev": "set HOST=dev && jest",
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- "test-local": "set HOST=localhost && jest"
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+ "lint": "eslint \"./src/**/*.ts\"",
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+ "lint-fix": "eslint \"./src/**/*.ts\" --fix",
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+ "test": "grok test",
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+ "test-dev": "grok test --host dev",
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+ "test-local": "grok test --host localhost"
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  },
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- "sources": [
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- "css/style.css",
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- "vendors/openchemlib-full.js"
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+ "canEdit": [
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+ "Developers"
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+ ],
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+ "canView": [
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+ "All users"
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  ],
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  "category": "Bioinformatics"
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  }