@datagrok/sequence-translator 1.0.16 → 1.1.0

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 (92) hide show
  1. package/.eslintrc.json +4 -3
  2. package/CHANGELOG.md +3 -0
  3. package/detectors.js +8 -28
  4. package/dist/package-test.js +2 -72987
  5. package/dist/package-test.js.map +1 -0
  6. package/dist/package.js +2 -72192
  7. package/dist/package.js.map +1 -0
  8. package/files/axolabs-style.json +97 -0
  9. package/files/codes-to-symbols.json +66 -0
  10. package/files/formats-to-helm.json +59 -0
  11. package/files/linkers.json +22 -0
  12. package/files/monomer-lib.json +1094 -0
  13. package/link-bio +7 -0
  14. package/package.json +30 -26
  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 → model/axolabs}/draw-svg.ts +1 -1
  21. package/src/{axolabs → model/axolabs}/helpers.ts +7 -5
  22. package/src/model/const.ts +19 -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 +48 -0
  28. package/src/model/format-translation/format-converter.ts +107 -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 +106 -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/{structures-works → model/sequence-to-structure-utils}/mol-transformations.ts +61 -87
  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 +94 -0
  38. package/src/model/sequence-to-structure-utils/sequence-to-molfile.ts +409 -0
  39. package/src/package.ts +106 -77
  40. package/src/tests/const.ts +17 -0
  41. package/src/tests/smiles-tests.ts +32 -457
  42. package/src/view/const/main-tab.ts +3 -0
  43. package/src/view/const/view.ts +10 -0
  44. package/src/view/css/axolabs-tab.css +1 -0
  45. package/src/view/css/colored-text-input.css +27 -0
  46. package/src/view/css/main-tab.css +46 -0
  47. package/src/view/css/sdf-tab.css +39 -0
  48. package/src/view/monomer-lib-viewer/viewer.ts +22 -0
  49. package/src/view/tabs/axolabs.ts +720 -0
  50. package/src/view/tabs/main.ts +174 -0
  51. package/src/view/tabs/sdf.ts +173 -0
  52. package/src/view/utils/app-info-dialog.ts +18 -0
  53. package/src/view/utils/colored-input/colored-text-input.ts +56 -0
  54. package/src/view/utils/colored-input/input-painters.ts +44 -0
  55. package/src/view/utils/draw-molecule.ts +86 -0
  56. package/src/view/utils/molecule-img.ts +106 -0
  57. package/src/view/view.ts +129 -0
  58. package/tsconfig.json +12 -18
  59. package/webpack.config.js +17 -4
  60. package/README.md +0 -84
  61. package/css/style.css +0 -18
  62. package/img/Sequence Translator Axolabs.png +0 -0
  63. package/jest.config.js +0 -33
  64. package/setup-unlink-clean.cmd +0 -14
  65. package/setup.cmd +0 -14
  66. package/setup.sh +0 -37
  67. package/src/__jest__/remote.test.ts +0 -77
  68. package/src/__jest__/test-node.ts +0 -97
  69. package/src/apps/oligo-sd-file-app.ts +0 -58
  70. package/src/autostart/ICDs.ts +0 -3
  71. package/src/autostart/IDPs.ts +0 -3
  72. package/src/autostart/calculations.ts +0 -40
  73. package/src/autostart/constants.ts +0 -37
  74. package/src/autostart/registration.ts +0 -241
  75. package/src/autostart/salts.ts +0 -2
  76. package/src/autostart/sources.ts +0 -3
  77. package/src/autostart/users.ts +0 -3
  78. package/src/axolabs/constants.ts +0 -101
  79. package/src/axolabs/define-pattern.ts +0 -873
  80. package/src/helpers.ts +0 -28
  81. package/src/main/main-view.ts +0 -262
  82. package/src/structures-works/const.ts +0 -5
  83. package/src/structures-works/converters.ts +0 -323
  84. package/src/structures-works/from-monomers.ts +0 -267
  85. package/src/structures-works/map.ts +0 -720
  86. package/src/structures-works/save-sense-antisense.ts +0 -91
  87. package/src/structures-works/sequence-codes-tools.ts +0 -344
  88. package/src/utils/parse.ts +0 -27
  89. package/src/utils/sdf-add-columns.ts +0 -118
  90. package/src/utils/sdf-save-table.ts +0 -56
  91. package/test-SequenceTranslator-6288c2fbe346-cce4ac1d.html +0 -259
  92. package/vendors/openchemlib-full.js +0 -293
package/test-SequenceTranslator-6288c2fbe346-cce4ac1d.html DELETED
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- </style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=6288c2fbe346. Commit cce4ac1d.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-12-12 14:55:37</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">21.067s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">6.276s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)
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- at Generator.next (&lt;anonymous&gt;)
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- at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:28:58)
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- at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:40:11
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- at Generator.next (&lt;anonymous&gt;)
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- at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:31:71
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- at new Promise (&lt;anonymous&gt;)
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- at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:27:12)
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- at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:38:23)
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- at Promise.then.completed (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/jest-circus/build/utils.js:391:28)
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- at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing SequenceTranslator package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:72:11
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- at Generator.next (&lt;anonymous&gt;)
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- at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
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- at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 2 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
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- Test result : Success : 0 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
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- Test result : Success : 0 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
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- Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu : OK
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- Test result : Success : 0 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
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- Test result : Success : 1 : SequenceTranslator.sequence-translator.acacacsacsac : OK
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- Test result : Success : 0 : SequenceTranslator.sequence-translator.cccgggusug : OK
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- Test result : Success : 0 : SequenceTranslator.sequence-translator.UfAfCfGfGfCfAfUf : OK
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- Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
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- Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
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- Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
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- </pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:74:11
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- at Generator.next (&lt;anonymous&gt;)
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- at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
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- at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message"/></div></div></div></div></body></html>