grnsight 6.0.7 → 7.2.0

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 (67) hide show
  1. package/.eslintrc.yml +4 -4
  2. package/.github/workflows/node.js.yml +35 -0
  3. package/README.md +1 -1
  4. package/database/README.md +218 -97
  5. package/database/constants.py +42 -0
  6. package/database/filter_update.py +168 -0
  7. package/database/grnsettings-database/README.md +52 -0
  8. package/database/grnsettings-database/schema.sql +4 -0
  9. package/database/loader.py +30 -0
  10. package/database/loader_update.py +36 -0
  11. package/database/network-database/scripts/generate_network.py +15 -23
  12. package/database/network-database/scripts/generate_new_network_version.py +17 -24
  13. package/database/protein-protein-database/README.md +71 -0
  14. package/database/protein-protein-database/schema.sql +37 -0
  15. package/database/protein-protein-database/scripts/generate_protein_network.py +227 -0
  16. package/database/protein-protein-database/scripts/remove_duplicates.sh +4 -0
  17. package/database/utils.py +418 -0
  18. package/package.json +3 -2
  19. package/server/app.js +2 -0
  20. package/server/config/config.js +4 -4
  21. package/server/controllers/additional-sheet-parser.js +2 -1
  22. package/server/controllers/constants.js +5 -0
  23. package/server/controllers/custom-workbook-controller.js +4 -3
  24. package/server/controllers/demo-workbooks.js +1462 -6
  25. package/server/controllers/export-constants.js +3 -2
  26. package/server/controllers/exporters/sif.js +6 -1
  27. package/server/controllers/exporters/xlsx.js +8 -3
  28. package/server/controllers/expression-sheet-parser.js +0 -6
  29. package/server/controllers/grnsettings-database-controller.js +17 -0
  30. package/server/controllers/importers/sif.js +30 -11
  31. package/server/controllers/network-database-controller.js +2 -2
  32. package/server/controllers/network-sheet-parser.js +54 -12
  33. package/server/controllers/protein-database-controller.js +18 -0
  34. package/server/controllers/sif-constants.js +11 -4
  35. package/server/controllers/spreadsheet-controller.js +44 -1
  36. package/server/controllers/workbook-constants.js +21 -4
  37. package/server/dals/expression-dal.js +4 -4
  38. package/server/dals/grnsetting-dal.js +49 -0
  39. package/server/dals/network-dal.js +14 -15
  40. package/server/dals/protein-dal.js +106 -0
  41. package/test/additional-sheet-parser-tests.js +1 -1
  42. package/test/export-tests.js +136 -9
  43. package/test/import-sif-tests.js +67 -13
  44. package/test/test.js +1 -1
  45. package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
  46. package/test-files/demo-files/18_proteins_81_edges_PPI.xlsx +0 -0
  47. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  48. package/web-client/config/config.js +4 -4
  49. package/web-client/public/js/api/grnsight-api.js +18 -3
  50. package/web-client/public/js/constants.js +27 -12
  51. package/web-client/public/js/generateNetwork.js +170 -72
  52. package/web-client/public/js/graph.js +424 -161
  53. package/web-client/public/js/grnsight.js +25 -4
  54. package/web-client/public/js/grnstate.js +4 -1
  55. package/web-client/public/js/iframe-coordination.js +3 -3
  56. package/web-client/public/js/setup-handlers.js +76 -61
  57. package/web-client/public/js/setup-load-and-import-handlers.js +32 -7
  58. package/web-client/public/js/update-app.js +119 -28
  59. package/web-client/public/js/upload.js +142 -85
  60. package/web-client/public/js/warnings.js +25 -0
  61. package/web-client/public/lib/bootstrap.file-input/bootstrap.file-input.js +0 -1
  62. package/web-client/public/stylesheets/grnsight.styl +40 -16
  63. package/web-client/views/components/demo.pug +7 -5
  64. package/web-client/views/upload.pug +64 -50
  65. package/database/network-database/scripts/filter_genes.py +0 -76
  66. package/database/network-database/scripts/loader.py +0 -79
  67. package/database/network-database/scripts/loader_updates.py +0 -99
package/server/controllers/demo-workbooks.js CHANGED
@@ -1,3 +1,5 @@
1
+ const constants = require("./constants");
2
+
1
3
  /* eslint-disable camelcase */
2
4
  var helpers = require(__dirname + "/helpers");
3
5
 
@@ -513,7 +515,7 @@ var demoWorkbook1 = function (path, res, app) {
513
515
  },
514
516
  meta: {
515
517
  data: {
516
- alpha: 0.002,
518
+ alpha: 0.02,
517
519
  kk_max: 1,
518
520
  MaxIter: 100000000,
519
521
  TolFun: 0.000001,
@@ -529,7 +531,8 @@ var demoWorkbook1 = function (path, res, app) {
529
531
  Strain: ["wt", "dcin5", "dgln3", "dhap4", "dhmo1", "dzap1"],
530
532
  simulation_timepoints: [0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60],
531
533
  species: "Saccharomyces cerevisiae",
532
- taxon_id: 559292
534
+ taxon_id: 559292,
535
+ workbookType: constants.NETWORK_GRN_MODE
533
536
  }
534
537
  },
535
538
  twoColumnSheets: {
@@ -2676,7 +2679,7 @@ var demoWorkbook2 = function (path, res, app) {
2676
2679
  },
2677
2680
  meta: {
2678
2681
  data: {
2679
- alpha: 0.002,
2682
+ alpha: 0.02,
2680
2683
  kk_max: 1,
2681
2684
  MaxIter: 100000000,
2682
2685
  TolFun: 0.000001,
@@ -2692,7 +2695,8 @@ var demoWorkbook2 = function (path, res, app) {
2692
2695
  Strain: ["wt", "dcin5", "dgln3", "dhap4", "dhmo1", "dzap1"],
2693
2696
  simulation_timepoints: [0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60],
2694
2697
  species: "Saccharomyces cerevisiae",
2695
- taxon_id: 559292
2698
+ taxon_id: 559292,
2699
+ workbookType: constants.NETWORK_GRN_MODE
2696
2700
  }
2697
2701
  },
2698
2702
  twoColumnSheets: {
@@ -4619,7 +4623,8 @@ var demoWorkbook3 = function (path, res, app) {
4619
4623
  MaxFunEval: 1000000,
4620
4624
  TolX: 0.00001,
4621
4625
  species: "Saccharomyces cerevisiae",
4622
- taxon_id: 559292
4626
+ taxon_id: 559292,
4627
+ workbookType: constants.NETWORK_GRN_MODE
4623
4628
  }
4624
4629
  },
4625
4630
  twoColumnSheets: {},
@@ -5680,7 +5685,8 @@ var demoWorkbook4 = function (path, res, app) {
5680
5685
  MaxFunEval: 1000000,
5681
5686
  TolX: 0.00001,
5682
5687
  species: "Saccharomyces cerevisiae",
5683
- taxon_id: 559292
5688
+ taxon_id: 559292,
5689
+ workbookType: constants.NETWORK_GRN_MODE
5684
5690
  }
5685
5691
  },
5686
5692
  twoColumnSheets: {},
@@ -5960,6 +5966,1454 @@ var demoWorkbook4 = function (path, res, app) {
5960
5966
  return processDemo(path, res, app, workbook4);
5961
5967
  };
5962
5968
 
5969
+ var demoWorkbook5 = function (path, res, app) {
5970
+ let workbook5 = {
5971
+ genes: [
5972
+ {
5973
+ name: "Aim32p",
5974
+ },
5975
+ {
5976
+ name: "Ccr4p",
5977
+ },
5978
+ {
5979
+ name: "Erv1p",
5980
+ },
5981
+ {
5982
+ name: "Fbp1p",
5983
+ },
5984
+ {
5985
+ name: "Hsc82p",
5986
+ },
5987
+ {
5988
+ name: "Hsp78p",
5989
+ },
5990
+ {
5991
+ name: "Mia40p",
5992
+ },
5993
+ {
5994
+ name: "Mpt5p",
5995
+ },
5996
+ {
5997
+ name: "Nab2p",
5998
+ },
5999
+ {
6000
+ name: "Osm1p",
6001
+ },
6002
+ {
6003
+ name: "Puf3p",
6004
+ },
6005
+ {
6006
+ name: "Sod2p",
6007
+ },
6008
+ {
6009
+ name: "Srp54p",
6010
+ },
6011
+ {
6012
+ name: "Ssc1p",
6013
+ },
6014
+ {
6015
+ name: "Tim17p",
6016
+ },
6017
+ {
6018
+ name: "Tim22p",
6019
+ },
6020
+ {
6021
+ name: "Tim23p",
6022
+ },
6023
+ {
6024
+ name: "Tim50p",
6025
+ },
6026
+ ],
6027
+ links: [
6028
+ {
6029
+ source: 0,
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+ target: 1,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ source: 1,
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+ target: 1,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ source: 0,
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+ target: 2,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ source: 2,
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+ target: 2,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ source: 0,
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+ target: 3,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ source: 3,
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+ target: 3,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ target: 5,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
6090
+ },
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+ {
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+ source: 1,
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+ target: 5,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ source: 4,
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+ target: 5,
6101
+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ type: "arrowhead",
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+ stroke: "black",
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+ type: "arrowhead",
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ target: 6,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ source: 0,
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+ target: 7,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ source: 1,
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+ target: 7,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ target: 7,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ target: 7,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ },
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+ type: "arrowhead",
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+ },
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+ type: "arrowhead",
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+ stroke: "black",
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ target: 8,
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+ value: 1,
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ type: "arrowhead",
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+ stroke: "black",
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+ },
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+ {
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+ type: "arrowhead",
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+ },
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+ type: "arrowhead",
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+ type: "arrowhead",
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7414
+ return processDemo(path, res, app, workbook5);
7415
+ };
7416
+
5963
7417
  module.exports = function (path, res, app, workbook) {
5964
7418
  if (path === "test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_input.xlsx") {
5965
7419
  return demoWorkbook1(path, res, app, workbook);
@@ -5969,5 +7423,7 @@ module.exports = function (path, res, app, workbook) {
5969
7423
  return demoWorkbook3(path, res, app, workbook);
5970
7424
  } else if (path === "test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx") {
5971
7425
  return demoWorkbook4(path, res, app, workbook);
7426
+ } else if (path === "test-files/demo-files/18_proteins_81_edges_PPI.xlsx") {
7427
+ return demoWorkbook5(path, res, app, workbook);
5972
7428
  }
5973
7429
  };