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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- <a href="http://www.lmu.edu" target="_blank"><img src="/GRNsight/assets/images/LMULogoHQ2.png" alt="LMU logo" width="200" height="118" id="lmuLogo" /></a><br /><br /><br />
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- <p id="subtextLMU">A Joint Project of the<br /> LMU Bioinformatics and Biomathematics Groups</p>
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- </div>
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- <p id="title"><a href="/GRNsight">GRNsight</a></p>
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- <p id="subtext">Web app and service for visualizing models of gene regulatory networks.</p>
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- <div class="alert alert-success d-none" id="cookie-notice" role="alert">
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- <div>This site uses Google Analytics to count pageviews and file uploads to demonstrate usage of our software to interested parties such as our employers and funding agencies. Information about your use of this site is shared with Google. By using this site, you agree to its use of cookies.</div>
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- <button class="cookie-action" data-dismiss="alert" aria-label="Got It">
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- <strong>Got It</strong>
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- </button>
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- <a target="_blank" class="cookie-action" href="https://www.google.com/policies/technologies/cookies/">
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- <div id="navBar" class=".backBox">
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- <li><a href="/GRNsight/">Home</a></li>
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- <li><a href="/GRNsight/about.html">About</a></li>
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- <li><a href="/GRNsight/news.html">News</a></li>
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- <li><a href="/GRNsight/people.html">People</a></li>
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- The remote/online GRNsight team at one of our weekly meetings
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- on 11 September 2020<!-- 10:43 am -->. <em>Clockwise from top left:</em>
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- Ian M. Green, John David N. Dionisio, Kam Dahlquist, Ona O. Igbinedion,
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- The Dahlquist Lab along with the LMU Bioinformatics and
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- Biomathematics Groups at the
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- <em>Front row, left to right:</em> Monica Hong, Nicole Anguiano,
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- Anindita Varshneya, Trixie Roque, John David N. Dionisio.
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- src="/GRNsight/assets/images/Choe-Shin_CMSI402-poster-session_20180430.jpg"
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- <p id="pageTitle">People</p>
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- <section>
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- <h2>Principal Investigators</h2>
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- <p class="name">Kam D. Dahlquist, Ph.D.</p>
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- <a href="http://kdahlquist.github.io/DahlquistLab/" target="_blank">http://kdahlquist.github.io/DahlquistLab/</a> <br>
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- Department of Biology</p><br>
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- <p class="name">John David N. Dionisio, Ph.D.</p>
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- <a href="http://dondi.lmu.build/" target="_blank">http://dondi.lmu.build/</a> <br>
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- Department of Computer Science</p> <br>
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- <p class="name">Ben G. Fitzpatrick, Ph.D.</p>
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- Department of Mathematics
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- <h2>Manager of Laboratory Facilities</h2>
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- <p class="name">Masao Kitamura</p>
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- <p class="personInfo">Department of Computer Science</p>
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- </section>
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- <h2>Research Assistants</h2>
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- <p class="name">Current Students</p>
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- <p class="studentName">Ona O. Igbinedion (LMU Computer Science '22) Spring 2020 - Present</p>
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- <p class="studentName">Ian M. Green (LMU Computer Science '22) Fall 2020 - Present</p>
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- <p class="studentName">Lauren L. Amparo (LMU Biology '24) Fall 2020 - Present</p>
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- <p class="name">Former Students</p>
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- <p class="studentName">Alexia M. Filler (LMU Computer Science '20) Spring 2019 - Spring 2020</p>
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- <p class="studentName">Kevin B. Patterson (LMU Computer Science '20) Spring 2020 - Spring 2020</p>
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