grnsight 6.0.4 → 7.1.1

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 (1245) hide show
  1. package/.eslintrc.yml +4 -4
  2. package/database/README.md +224 -79
  3. package/database/constants.py +42 -0
  4. package/database/expression-database/README.md +2 -2
  5. package/database/expression-database/schema.sql +14 -14
  6. package/database/expression-database/scripts/loader.py +6 -6
  7. package/database/filter_update.py +168 -0
  8. package/database/grnsettings-database/README.md +52 -0
  9. package/database/grnsettings-database/schema.sql +4 -0
  10. package/database/loader.py +30 -0
  11. package/database/loader_update.py +36 -0
  12. package/database/network-database/README.md +36 -4
  13. package/database/network-database/schema.sql +7 -7
  14. package/database/network-database/scripts/generate_network.py +16 -24
  15. package/database/network-database/scripts/generate_new_network_version.py +216 -0
  16. package/database/protein-protein-database/README.md +71 -0
  17. package/database/protein-protein-database/schema.sql +37 -0
  18. package/database/protein-protein-database/scripts/generate_protein_network.py +227 -0
  19. package/database/protein-protein-database/scripts/remove_duplicates.sh +4 -0
  20. package/database/utils.py +418 -0
  21. package/package.json +2 -2
  22. package/server/app.js +2 -0
  23. package/server/config/config.js +4 -4
  24. package/server/controllers/additional-sheet-parser.js +2 -1
  25. package/server/controllers/constants.js +5 -0
  26. package/server/controllers/custom-workbook-controller.js +8 -6
  27. package/server/controllers/demo-workbooks.js +1460 -4
  28. package/server/controllers/export-constants.js +3 -2
  29. package/server/controllers/exporters/sif.js +6 -1
  30. package/server/controllers/exporters/xlsx.js +8 -3
  31. package/server/controllers/expression-sheet-parser.js +0 -6
  32. package/server/controllers/grnsettings-database-controller.js +17 -0
  33. package/server/controllers/importers/sif.js +29 -11
  34. package/server/controllers/network-database-controller.js +2 -2
  35. package/server/controllers/network-sheet-parser.js +54 -12
  36. package/server/controllers/protein-database-controller.js +18 -0
  37. package/server/controllers/sif-constants.js +4 -4
  38. package/server/controllers/spreadsheet-controller.js +44 -1
  39. package/server/controllers/workbook-constants.js +21 -4
  40. package/server/dals/expression-dal.js +8 -7
  41. package/server/dals/grnsetting-dal.js +49 -0
  42. package/server/dals/network-dal.js +13 -12
  43. package/server/dals/protein-dal.js +106 -0
  44. package/test/export-tests.js +136 -9
  45. package/test/import-sif-tests.js +54 -13
  46. package/test/test.js +1 -1
  47. package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
  48. package/test-files/demo-files/18_proteins_81_edges_PPI.xlsx +0 -0
  49. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  50. package/web-client/config/config.js +4 -4
  51. package/web-client/public/js/api/grnsight-api.js +72 -56
  52. package/web-client/public/js/constants.js +26 -12
  53. package/web-client/public/js/generateNetwork.js +173 -67
  54. package/web-client/public/js/graph.js +420 -150
  55. package/web-client/public/js/grnsight.js +25 -4
  56. package/web-client/public/js/grnstate.js +3 -1
  57. package/web-client/public/js/iframe-coordination.js +3 -3
  58. package/web-client/public/js/setup-handlers.js +28 -32
  59. package/web-client/public/js/setup-load-and-import-handlers.js +196 -170
  60. package/web-client/public/js/update-app.js +84 -17
  61. package/web-client/public/js/upload.js +193 -157
  62. package/web-client/public/lib/bootstrap.file-input/bootstrap.file-input.js +0 -1
  63. package/web-client/public/stylesheets/grnsight.styl +40 -16
  64. package/web-client/views/components/demo.pug +7 -5
  65. package/web-client/views/upload.pug +63 -49
  66. package/.bundle/config +0 -3
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  68. package/Gemfile.lock +0 -259
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- <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var xmlbuilder = require("xmlbuilder");
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- var constants = require(__dirname + "/../constants");
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- var INTERACTION_ID = "interaction";
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- var NAME_ID = "name";
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- var WEIGHT_ID = "weight";
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- &nbsp;
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- var grnsightToGraphMlJson = function (network) {
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- "#comment": "Exported by GRNsight v" + constants.VERSION + " " +
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- "http://dondi.github.io/GRNsight/ " +
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- "https://github.com/dondi/GRNsight/releases/tag/v" + constants.VERSION,
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- &nbsp;
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- key: [
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- {
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- "@id": NAME_ID,
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- "@for": "node",
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- "@attr.name": "name",
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- "@attr.type": "string"
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- },
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- &nbsp;
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- {
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- "@id": INTERACTION_ID,
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- "@for": "edge",
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- "@attr.name": "interaction",
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- "@attr.type": "string"
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- },
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- &nbsp;
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- {
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- "@id": NAME_ID,
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- "@attr.type": "string"
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- }
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- ]
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- }
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- };
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- &nbsp;
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- if (network.sheetType === constants.WEIGHTED) {
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- "@id": WEIGHT_ID,
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- "@for": "edge",
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- "@attr.name": "weight",
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- "@attr.type": "double"
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- });
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- }
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- &nbsp;
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- convertedNetwork.graphml.graph = {
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- "@edgedefault": "directed",
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- &nbsp;
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- node: network.genes.map(function (gene) {
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- return {
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- "@id": gene.name,
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- data: {
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- "@key": NAME_ID,
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- "#text": gene.name
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- }
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- };
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- }),
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- &nbsp;
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- edge: network.links.map(function (link) {
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- var targetGeneId = network.genes[link.target].name;
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- &nbsp;
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- var edge = {
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- "@source": sourceGeneId,
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- "@target": targetGeneId,
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- data: [
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- {
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- "@key": INTERACTION_ID,
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- "#text": "pd"
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- },
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- &nbsp;
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- {
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- "@key": NAME_ID,
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- "#text": sourceGeneId + " (pd) " + targetGeneId
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- }
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- ]
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- };
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- &nbsp;
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- if (network.sheetType === constants.WEIGHTED) {
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- "@key": WEIGHT_ID,
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- "#text": link.value
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- });
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- }
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- &nbsp;
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- return edge;
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- })
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- };
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- &nbsp;
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- if (network.filename) {
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- convertedNetwork.graphml.graph["@id"] = network.filename;
372
- }
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- &nbsp;
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- return convertedNetwork;
375
- };
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- &nbsp;
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- module.exports = function (network) {
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- return xmlbuilder.create(grnsightToGraphMlJson(network), {
379
- version: "1.0",
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- encoding: "UTF-8"
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- }).end({
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- <span class="strong">100% </span>
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- <span class='fraction'>34/34</span>
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- <td data-value="100" class="pct high">100%</td>
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- <td data-value="22" class="abs high">22/22</td>
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- <td data-value="100" class="pct high">100%</td>
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- <td data-value="12" class="abs high">12/12</td>
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- <td data-value="100" class="pct high">100%</td>
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- <td data-value="100" class="pct high">100%</td>
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- <td data-value="4" class="abs high">4/4</td>
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- <td data-value="12" class="abs high">12/12</td>
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