grnsight 5.0.0 → 5.1.0

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 (189) hide show
  1. package/.travis.yml +1 -1
  2. package/package.json +5 -5
  3. package/server/app.js +4 -2
  4. package/server/controllers/database-controller.js +9 -8
  5. package/server/controllers/exporters/xlsx.js +27 -9
  6. package/test/export-tests.js +2 -2
  7. package/test/test.js +3 -1
  8. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  9. package/web-client/app.js +1 -1
  10. package/web-client/controllers/main.js +1 -1
  11. package/web-client/public/js/constants.js +4 -1
  12. package/web-client/public/js/update-app.js +8 -11
  13. package/web-client/public/js/upload.js +337 -11
  14. package/web-client/views/{graph.jade → graph.pug} +0 -0
  15. package/web-client/views/{info.jade → info.pug} +1 -5
  16. package/web-client/views/{upload.jade → upload.pug} +47 -4
  17. package/documents/SDF/CMSI_402/spring_2014/Southwick_CMSI402_Spring2014_software-development-plan.md +0 -71
  18. package/documents/SDF/CMSI_402/spring_2014/Southwick_CMSI402_Spring2014_software-requirements-specification.md +0 -71
  19. package/documents/SDF/CMSI_402/spring_2014/use-case-diagram-spring-2014.jpg +0 -0
  20. package/documents/SDF/CMSI_402/spring_2017/Anguiano_402_Final_Presentation.pptx +0 -0
  21. package/documents/SDF/CMSI_402/spring_2017/Anguiano_402_Presentation_Final_Poster.pdf +0 -0
  22. package/documents/SDF/CMSI_402/spring_2017/Anguiano_CMSI402_Spring2017_project-proposal-presentation.pptx +0 -0
  23. package/documents/SDF/CMSI_402/spring_2017/Anguiano_CMSI402_Spring2017_project-proposal.docx +0 -0
  24. package/documents/SDF/CMSI_402/spring_2017/Anguiano_CMSI402_Spring2017_software-development-plan.docx +0 -0
  25. package/documents/SDF/CMSI_402/spring_2017/Anguiano_CMSI402_Spring2017_software-requirements-specification.docx +0 -0
  26. package/documents/SDF/CMSI_402/spring_2017/Design Review Presentation.pptx +0 -0
  27. package/documents/SDF/CMSI_402/spring_2018/0402report.docx +0 -0
  28. package/documents/SDF/CMSI_402/spring_2018/0409report.docx +0 -0
  29. package/documents/SDF/CMSI_402/spring_2018/402-gantt.png +0 -0
  30. package/documents/SDF/CMSI_402/spring_2018/402SRS_GRNSightFeedback01.txt +0 -28
  31. package/documents/SDF/CMSI_402/spring_2018/402_SPD.md +0 -223
  32. package/documents/SDF/CMSI_402/spring_2018/ChoeShinCMSI402_Final.pptx +0 -0
  33. package/documents/SDF/CMSI_402/spring_2018/ProjectProposal.md +0 -22
  34. package/documents/SDF/CMSI_402/spring_2018/SoftwareRequirementsSpecification.md +0 -88
  35. package/documents/SDF/CMSI_402/spring_2018/homework/choe_eileen/Choe_Eileen_CMSI 402_HW1.pdf +0 -0
  36. package/documents/SDF/CMSI_402/spring_2018/homework/choe_eileen/Choe_Eileen_CMSI402_HW2.pdf +0 -0
  37. package/documents/SDF/CMSI_402/spring_2018/homework/shin_jen/402hw2.docx +0 -0
  38. package/documents/SDF/CMSI_402/spring_2018/homework/shin_jen/Jen - 402Hw1.docx +0 -0
  39. package/documents/SDF/CMSI_402/spring_2018/homework/shin_jen/Jen - hw3.docx +0 -0
  40. package/documents/SDF/CMSI_402/spring_2018/writtenStatusReport.docx +0 -0
  41. package/documents/SDF/CMSI_402/spring_2018/writtenStatusReport4 +0 -0
  42. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Expression Database Schema.pdf +0 -0
  43. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/ExpressionDbLayoutImage.jpg +0 -0
  44. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/ExpressionDbLayoutImageSmall.jpg +0 -0
  45. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Filler_Patterson_CMSI402_Poster.pptx +0 -0
  46. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/GRNsight Final Presentation.pdf +0 -0
  47. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Project Proposal Doc.pdf +0 -0
  48. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Project Proposal Presentation.pdf +0 -0
  49. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Software Development Plan/GANTT Chart.xlsx +0 -0
  50. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Software Development Plan/Software Development Plan.pdf +0 -0
  51. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Software Development Plan (Updated)/GANTT Chart (Updated).xlsx +0 -0
  52. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Software Development Plan (Updated)/Software Development Plan (Updated).pdf +0 -0
  53. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Software Requirements Specification (Updated).pdf +0 -0
  54. package/documents/SDF/CMSI_402/spring_2020/Alexia Filler/Software Requirements Specification.pdf +0 -0
  55. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/402 GANTT Chart - Sheet1.pdf +0 -0
  56. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/402 GRNsight SDP.pdf +0 -0
  57. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/402 SRS.pdf +0 -0
  58. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/FINAL GRNSIGHT PRESENTATION.pdf +0 -0
  59. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/GRNsight Presentation.pdf +0 -0
  60. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/Project Proposal 402.pdf +0 -0
  61. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/SDP Updated/402 GANTT Chart UPDATED - Sheet1.pdf +0 -0
  62. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/SDP Updated/402 GRNsight SDP UPDATED.pdf +0 -0
  63. package/documents/SDF/CMSI_402/spring_2020/Kevin Patterson/SRS Update/402 SRS Final.pdf +0 -0
  64. package/documents/abstracts/Anguiano_Varshneya_Undergraduate-Research-Symposium_2017_abstract.pdf +0 -0
  65. package/documents/abstracts/Dahlquist_Dionisio_et-al_BOSC_2020_abstract.pdf +0 -0
  66. package/documents/abstracts/SIGGRAPH 2017 Abstract/ACM-Reference-Format.bst +0 -3478
  67. package/documents/abstracts/SIGGRAPH 2017 Abstract/Figure1_zoom100.png +0 -0
  68. package/documents/abstracts/SIGGRAPH 2017 Abstract/acmart.cls +0 -2352
  69. package/documents/abstracts/SIGGRAPH 2017 Abstract/acmart.ins +0 -29
  70. package/documents/abstracts/SIGGRAPH 2017 Abstract/always-weights.png +0 -0
  71. package/documents/abstracts/SIGGRAPH 2017 Abstract/auto.png +0 -0
  72. package/documents/abstracts/SIGGRAPH 2017 Abstract/networkA.png +0 -0
  73. package/documents/abstracts/SIGGRAPH 2017 Abstract/networkB-normalized.png +0 -0
  74. package/documents/abstracts/SIGGRAPH 2017 Abstract/networkB.png +0 -0
  75. package/documents/abstracts/SIGGRAPH 2017 Abstract/never-weights.png +0 -0
  76. package/documents/abstracts/SIGGRAPH 2017 Abstract/representative-image/screenshot.jpg +0 -0
  77. package/documents/abstracts/SIGGRAPH 2017 Abstract/representative-image/screenshot3x2.png +0 -0
  78. package/documents/abstracts/SIGGRAPH 2017 Abstract/representative-image/withweights3x2.png +0 -0
  79. package/documents/abstracts/SIGGRAPH 2017 Abstract/screenshot-auto.png +0 -0
  80. package/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.bib +0 -85
  81. package/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.pdf +0 -0
  82. package/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.tex +0 -235
  83. package/documents/abstracts/SWE Collegiate Competition 2017.md +0 -9
  84. package/documents/abstracts/Samdarshi_GRNsight_SoCalSysBio_Abstract_2019.docx +0 -0
  85. package/documents/abstracts/Varshneya_Samdarshi_Southern-California-Systems-Biology_2017_abstract.docx +0 -0
  86. package/documents/abstracts/~$mdarshi_SoCalSysBio_Abstract_2019.docx +0 -0
  87. package/documents/developer_documents/State Diagram.graphml +0 -3525
  88. package/documents/developer_documents/graphml/State Diagram.graphml +0 -3115
  89. package/documents/developer_documents/older_versions/GRNsight State Diagram old.png +0 -0
  90. package/documents/developer_documents/older_versions/GRNsight State Diagram.png +0 -0
  91. package/documents/developer_documents/testing_script_generator/GRNsightTestingDocument.md +0 -1016
  92. package/documents/developer_documents/testing_script_generator/edgeFeatures.json +0 -178
  93. package/documents/developer_documents/testing_script_generator/fileFeatures.json +0 -100
  94. package/documents/developer_documents/testing_script_generator/layoutFeatures.json +0 -166
  95. package/documents/developer_documents/testing_script_generator/nodeFeatures.json +0 -195
  96. package/documents/developer_documents/testing_script_generator/speciesFeatures.json +0 -30
  97. package/documents/developer_documents/testing_script_generator/testing-script-generator.js +0 -172
  98. package/documents/developer_documents/testing_script_generator/viewFeatures.json +0 -82
  99. package/documents/developer_documents/testing_script_generator/viewportFeatures.json +0 -50
  100. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_conference-presentations_2016.docx +0 -0
  101. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016.docx +0 -0
  102. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016_Table1.docx +0 -0
  103. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016_references.rtf +0 -264
  104. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016_text-only.docx +0 -0
  105. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/21-genes_31-edges_Schade-data_for-screenshots.xlsx +0 -0
  106. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure1_zoom100.jpg +0 -0
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  120. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5A.pdf +0 -0
  121. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5B.pdf +0 -0
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  129. package/documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure3_GRNsight-Architecture.pdf +0 -0
  130. package/documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure4_GRNsight-Screenshot.pdf +0 -0
  131. package/documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure5_compiled.pdf +12 -5383
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  133. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_conference-presentations_2016_revised.docx +0 -0
  134. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_cover-letter-and-response_2016.pdf +0 -0
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  137. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_Table1.docx +0 -0
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  143. package/documents/manuscripts/peerj-computerscience-2016/revisions/figures/Figure3_GRNsight-Architecture.pdf +0 -0
  144. package/documents/manuscripts/peerj-computerscience-2016/revisions/figures/Figure4_GRNsight-Screenshot-auto.pdf +0 -0
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  146. package/documents/manuscripts/peerj-computerscience-2016/revisions/peerj-reviewing-10823-v1.pdf +0 -0
  147. package/documents/posters/Anguiano_CMSI402_2017.pptx +0 -0
  148. package/documents/posters/Anguiano_Varshneya_LMU-Symposium_2015.pptx +0 -0
  149. package/documents/posters/Anguiano_Varshneya_SCCUR_2014.pptx +0 -0
  150. package/documents/posters/Choe_Shin_CMSI402_2018.pptx +0 -0
  151. package/documents/posters/Dahlquist-et-al_BOSC_ISMB_2016_poster.pptx +0 -0
  152. package/documents/posters/Filler_Patterson_CMSI402_Poster.pptx +0 -0
  153. package/documents/posters/Igbinedion_Green_Mersaghian_LMU_SYMPOSIUM_2021.pptx +0 -0
  154. package/documents/posters/Lopez_Filler_LMU_Symposium_2019.pdf +0 -0
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  158. package/documents/posters/Samdarshi-et-al_SoCalSysBio_2019.pptx +0 -0
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  167. package/documents/presentations/Dahlquist_ExperimentalBiology_20160404_talk.pptx +0 -0
  168. package/documents/presentations/Dahlquist_GRNsight_BCC2020_20200720_lightning-talk_video.mp4 +0 -0
  169. package/documents/presentations/Dahlquist_SoCalSysBio_20150131_talk.pptx +0 -0
  170. package/documents/presentations/Filler_Patterson_CMSI402_Presentation_20200501.pdf +0 -0
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  172. package/documents/presentations/Samdarshi_LMU-Symposium_20190323_talk.pdf +0 -0
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  174. package/documents/presentations/Southwick_Anguiano_LMU-Symposium_20140329_talk.pptx +0 -0
  175. package/documents/presentations/Southwick_CMSI402_Presentation_20140508_talk.pptx +0 -0
  176. package/documents/presentations/Varshneya_Anguiano_LMU-Symposium_201703_talk.pptx +0 -0
  177. package/documents/reports/Samdarshi_Mihir_2019/Samdarshi_2019_Final.docx +0 -0
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