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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- VERSION: "2.10",
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- NOT_FOUND: -1,
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- WEIGHTED: "weighted",
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- errorDescription: "GRNsight has detected that one or more edges in your network are missing numerical" +
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- " weight values. Because the algorithm GRNsight uses for determining the arrowhead type and the color and" +
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- EDGE_DEFAULT_NOT_DIRECTED: {
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- warningCode: "SIF_FORMAT_WARNING",
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- errorDescription: " GRNsight has detected that there are no tabs in your file. The GRNsight specification" +
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- " for SIF files states that data must be delimited by tabs. Please review your data. This warning may" +
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- " suggest that your SIF file has comma separated data or contains no data at all. Additionally, valid" +
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- " networks which consist of single source nodes may also trigger this warning."
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- }
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- },
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- errors: {
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- SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR: {
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- errorCode: "SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR",
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- possibleCause: "The SIF importer detects an unweighted network with an unsupported relationship type.",
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- suggestedFix: "SIF files accepted by GRNsight must use 'pd' as the text string for the relationship type" +
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- " in unweighted networks. Please review the SIF input documentation. Additionally, this error may be have" +
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- " been caused by missing data in your file, which caused the importer to incorrectly interpret a source" +
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- " or target as the relationship."
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- },
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- errorCode: "SIF_MISSING_DATA_ERROR",
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- possibleCause: "GRNsight has detected that your SIF file contains missing data. ",
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- errorCode: "SIF_STRAY_DATA_ERROR",
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- possibleCause: "GRNsight has detected stray data and/or extraneous blank rows in your SIF file. ",
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- suggestedFix: "Please review the data and delete extraneous data from the file."
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- }
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- }
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- &nbsp;</pre></td></tr>
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- var grnsightToSif = require(__dirname + "/exporters/sif");
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- var grnsightToGraphMl = require(__dirname + "/exporters/graphml");
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- &nbsp;
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- <span class="cstat-no" title="statement not covered" > helpers.attachCorsHeader(res, app);</span>
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Disposition", "attachment;filename=\"" + req.body.filename + "\"");</span>
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- <span class="cstat-no" title="statement not covered" > return res.status(200).send(converter(JSON.parse(req.body.network)));</span>
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- };
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- &nbsp;
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- var generalExportError = <span class="fstat-no" title="function not covered" >fu</span>nction (res, error) {
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- <span class="cstat-no" title="statement not covered" > return res.json(400, {</span>
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- message: "Invalid GRNsight format.",
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- details: {
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- name: error.name,
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- message: error.message
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- }
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- });
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- };
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- &nbsp;
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- module.exports = function (app) {
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- <span class="missing-if-branch" title="if path not taken" >I</span>if (app) {
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- // The /convert-* routes represent pure data exchange;
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- // the /export-* ones wrap this around a file download.
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- <span class="cstat-no" title="statement not covered" > app.post("/convert-to-sif", <span class="fstat-no" title="function not covered" >fu</span>nction (req, res) {</span>
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Type", "text/plain");</span>
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Type", "text/plain");</span>
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- } catch (error) {
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- <span class="cstat-no" title="statement not covered" > return generalExportError(res, error);</span>
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- });
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- &nbsp;
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Type", "text/xml");</span>
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- <span class="cstat-no" title="statement not covered" > return convertResponse(app, req, res, grnsightToGraphMl);</span>
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- } catch (error) {
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- <span class="cstat-no" title="statement not covered" > return generalExportError(res, error);</span>
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- <span class="cstat-no" title="statement not covered" > res.header("Content-Type", "text/xml");</span>
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- <span class="cstat-no" title="statement not covered" > return exportResponse(app, req, res, grnsightToGraphMl);</span>
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- grnsightToSif: grnsightToSif,
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- grnsightToGraphMl: grnsightToGraphMl
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- &nbsp;</pre></td></tr>
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