grnsight 6.0.4 → 6.0.7
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.
- package/database/README.md +40 -16
- package/database/expression-database/README.md +2 -2
- package/database/expression-database/schema.sql +14 -14
- package/database/expression-database/scripts/loader.py +6 -6
- package/database/network-database/README.md +36 -4
- package/database/network-database/schema.sql +7 -7
- package/database/network-database/scripts/filter_genes.py +1 -1
- package/database/network-database/scripts/generate_network.py +1 -1
- package/database/network-database/scripts/generate_new_network_version.py +223 -0
- package/database/network-database/scripts/loader.py +3 -3
- package/database/network-database/scripts/loader_updates.py +99 -0
- package/package.json +2 -2
- package/server/controllers/custom-workbook-controller.js +4 -3
- package/server/dals/expression-dal.js +8 -7
- package/server/dals/network-dal.js +3 -3
- package/web-client/public/js/api/grnsight-api.js +56 -55
- package/web-client/public/js/generateNetwork.js +15 -7
- package/web-client/public/js/setup-load-and-import-handlers.js +171 -170
- package/web-client/public/js/upload.js +74 -95
- package/.bundle/config +0 -3
- package/GRNsight - Beta.html +0 -194
- package/Gemfile.lock +0 -259
- package/_gh_pages/about.html +0 -807
- package/_gh_pages/assets/css/bootstrap.min.css +0 -10
- package/_gh_pages/assets/css/footer.css +0 -3
- package/_gh_pages/assets/css/main.css +0 -363
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_3-edges-and-footer.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_header-and-3-nodes.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_output_3-edges-and-footer.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_output_header-and-3-nodes.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated_sif.png +0 -0
- package/_gh_pages/assets/images/Carrillo_Roque_LMU_Symposium_2015.pptx +0 -0
- package/_gh_pages/assets/images/Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
- package/_gh_pages/assets/images/Choe_SCCUR_2017.jpg +0 -0
- package/_gh_pages/assets/images/Dahlquist-BMB-2015-Fig1.jpg +0 -0
- package/_gh_pages/assets/images/Dahlquist-BMB-2015-Fig8.jpg +0 -0
- package/_gh_pages/assets/images/Dahlquist-Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
- package/_gh_pages/assets/images/Demo-3-auto-layout.jpg +0 -0
- package/_gh_pages/assets/images/Demo-3-paper-layout.jpg +0 -0
- package/_gh_pages/assets/images/Demo-4-auto-layout.jpg +0 -0
- package/_gh_pages/assets/images/Demo-4-paper-layout.jpg +0 -0
- package/_gh_pages/assets/images/Dionisio-Dahlquist_GRNsight-shades_20170506.jpg +0 -0
- package/_gh_pages/assets/images/GRNsight_logo_20140710_main.jpg +0 -0
- package/_gh_pages/assets/images/GRNsight_logo_20140710_main_resized.jpg +0 -0
- package/_gh_pages/assets/images/GRNsight_logo_20140710_rollover.jpg +0 -0
- package/_gh_pages/assets/images/GRNsight_logo_20140710_rollover_resized.jpg +0 -0
- package/_gh_pages/assets/images/Johnson_Williams_LMU_Symposium_2015.pptx +0 -0
- package/_gh_pages/assets/images/Klein_Samdarshi_TriBeta_2018_20180317.jpg +0 -0
- package/_gh_pages/assets/images/LMULogoHQ2.png +0 -0
- package/_gh_pages/assets/images/LMUSymposium_Group_20150321-2.jpg +0 -0
- package/_gh_pages/assets/images/LMUSymposium_Group_20150321-2_resized.jpg +0 -0
- package/_gh_pages/assets/images/Sample_network_optimized_weights_worksheet.jpg +0 -0
- package/_gh_pages/assets/images/Sample_network_worksheet.jpg +0 -0
- package/_gh_pages/assets/images/Shin_SCCUR_2017.jpg +0 -0
- package/_gh_pages/assets/images/demo-3_network-sheet.png +0 -0
- package/_gh_pages/assets/images/demo-4_network-optimized-weights-sheet.png +0 -0
- package/_gh_pages/assets/images/gene-pages-0.png +0 -0
- package/_gh_pages/assets/images/gene-pages-1.png +0 -0
- package/_gh_pages/assets/images/gene-pages-2.png +0 -0
- package/_gh_pages/assets/images/gene-pages-3.png +0 -0
- package/_gh_pages/assets/images/grnsight2020.png +0 -0
- package/_gh_pages/assets/images/lmu logo.gif +0 -0
- package/_gh_pages/assets/images/v3demo2-grid+nodecoloring.png +0 -0
- package/_gh_pages/assets/images/v3demo2-nodecoloring.png +0 -0
- package/_gh_pages/assets/images/v3demo2.png +0 -0
- package/_gh_pages/assets/js/ga-report.js +0 -35
- package/_gh_pages/assets/js/iframeResizer.min.js +0 -9
- package/_gh_pages/assets/js/main.js +0 -132
- package/_gh_pages/beta.html +0 -144
- package/_gh_pages/contact.html +0 -178
- package/_gh_pages/coverage/coverage.json +0 -1
- package/_gh_pages/coverage/coverage.raw.json +0 -1
- package/_gh_pages/coverage/lcov-report/base.css +0 -223
- package/_gh_pages/coverage/lcov-report/block-navigation.js +0 -63
- package/_gh_pages/coverage/lcov-report/controllers/additional-sheet-parser.js.html +0 -330
- package/_gh_pages/coverage/lcov-report/controllers/constants.js.html +0 -243
- package/_gh_pages/coverage/lcov-report/controllers/export-controller.js.html +0 -285
- package/_gh_pages/coverage/lcov-report/controllers/exporters/graphml.js.html +0 -405
- package/_gh_pages/coverage/lcov-report/controllers/exporters/index.html +0 -110
- package/_gh_pages/coverage/lcov-report/controllers/exporters/sif.js.html +0 -150
- package/_gh_pages/coverage/lcov-report/controllers/helpers.js.html +0 -114
- package/_gh_pages/coverage/lcov-report/controllers/import-controller.js.html +0 -233
- package/_gh_pages/coverage/lcov-report/controllers/importers/graphml.js.html +0 -716
- package/_gh_pages/coverage/lcov-report/controllers/importers/index.html +0 -106
- package/_gh_pages/coverage/lcov-report/controllers/importers/sif.js.html +0 -488
- package/_gh_pages/coverage/lcov-report/controllers/index.html +0 -162
- package/_gh_pages/coverage/lcov-report/controllers/semantic-checker.js.html +0 -810
- package/_gh_pages/coverage/lcov-report/controllers/spreadsheet-controller.js.html +0 -1779
- package/_gh_pages/coverage/lcov-report/index.html +0 -136
- package/_gh_pages/coverage/lcov-report/prettify.css +0 -1
- package/_gh_pages/coverage/lcov-report/prettify.js +0 -1
- package/_gh_pages/coverage/lcov-report/server/controllers/additional-sheet-parser.js.html +0 -330
- package/_gh_pages/coverage/lcov-report/server/controllers/constants.js.html +0 -243
- package/_gh_pages/coverage/lcov-report/server/controllers/export-controller.js.html +0 -285
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/graphml.js.html +0 -405
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/index.html +0 -110
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/sif.js.html +0 -150
- package/_gh_pages/coverage/lcov-report/server/controllers/graphml-constants.js.html +0 -585
- package/_gh_pages/coverage/lcov-report/server/controllers/helpers.js.html +0 -114
- package/_gh_pages/coverage/lcov-report/server/controllers/import-controller.js.html +0 -237
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/graphml.js.html +0 -585
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/index.html +0 -110
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/sif.js.html +0 -492
- package/_gh_pages/coverage/lcov-report/server/controllers/index.html +0 -188
- package/_gh_pages/coverage/lcov-report/server/controllers/semantic-checker.js.html +0 -810
- package/_gh_pages/coverage/lcov-report/server/controllers/spreadsheet-controller.js.html +0 -1779
- package/_gh_pages/coverage/lcov-report/sort-arrow-sprite.png +0 -0
- package/_gh_pages/coverage/lcov-report/sorter.js +0 -158
- package/_gh_pages/coverage/lcov-report/web-client/public/js/grnstate.js.html +0 -225
- package/_gh_pages/coverage/lcov-report/web-client/public/js/index.html +0 -97
- package/_gh_pages/coverage/lcov.info +0 -49
- package/_gh_pages/documentation.html +0 -1132
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.aux +0 -47
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.bbl +0 -73
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- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.synctex.gz +0 -0
- package/_gh_pages/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised-Dondi.docx +0 -0
- package/_gh_pages/encryption/server.cert +0 -21
- package/_gh_pages/encryption/server.key +0 -28
- package/_gh_pages/favicon.ico +0 -0
- package/_gh_pages/googlea1a858c5bc91c87e.html +0 -1
- package/_gh_pages/index.html +0 -163
- package/_gh_pages/links.html +0 -177
- package/_gh_pages/news.html +0 -367
- package/_gh_pages/onlyfooter.html +0 -78
- package/_gh_pages/onlyheader.html +0 -64
- package/_gh_pages/onlysidebar.html +0 -73
- package/_gh_pages/package-lock.json +0 -14048
- package/_gh_pages/params.json +0 -1
- package/_gh_pages/people.html +0 -260
- package/_gh_pages/privacy.html +0 -147
- package/_gh_pages/publications.html +0 -378
- package/_gh_pages/robots.txt +0 -1
- package/_gh_pages/server/API Project-7d45e9f24a96.p12 +0 -0
- package/_gh_pages/server/grnmap.pem +0 -31
- package/_gh_pages/server/grnsight.pem +0 -19
- package/_gh_pages/sitemap.xml +0 -174
- package/_gh_pages/test-files/import-samples/attributes.graphml +0 -40
- package/_gh_pages/test-files/import-samples/port.graphml +0 -32
- package/_gh_pages/test-files/import-samples/simple.graphml +0 -31
- package/_gh_pages/web-client/public/js/grnsight.min.js +0 -2347
- package/_gh_pages/web-client/public/stylesheets/grnsight.css +0 -443
- package/coverage/coverage.json +0 -1
- package/coverage/coverage.raw.json +0 -1
- package/coverage/lcov-report/base.css +0 -223
- package/coverage/lcov-report/block-navigation.js +0 -63
- package/coverage/lcov-report/controllers/additional-sheet-parser.js.html +0 -330
- package/coverage/lcov-report/controllers/constants.js.html +0 -243
- package/coverage/lcov-report/controllers/export-controller.js.html +0 -285
- package/coverage/lcov-report/controllers/exporters/graphml.js.html +0 -405
- package/coverage/lcov-report/controllers/exporters/index.html +0 -110
- package/coverage/lcov-report/controllers/exporters/sif.js.html +0 -150
- package/coverage/lcov-report/controllers/helpers.js.html +0 -114
- package/coverage/lcov-report/controllers/import-controller.js.html +0 -233
- package/coverage/lcov-report/controllers/importers/graphml.js.html +0 -716
- package/coverage/lcov-report/controllers/importers/index.html +0 -106
- package/coverage/lcov-report/controllers/importers/sif.js.html +0 -488
- package/coverage/lcov-report/controllers/index.html +0 -162
- package/coverage/lcov-report/controllers/semantic-checker.js.html +0 -810
- package/coverage/lcov-report/controllers/spreadsheet-controller.js.html +0 -1779
- package/coverage/lcov-report/index.html +0 -136
- package/coverage/lcov-report/prettify.css +0 -1
- package/coverage/lcov-report/prettify.js +0 -1
- package/coverage/lcov-report/server/controllers/additional-sheet-parser.js.html +0 -330
- package/coverage/lcov-report/server/controllers/constants.js.html +0 -243
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- package/encryption/server.cert +0 -21
- package/encryption/server.key +0 -28
- package/gdb/PG_VERSION +0 -1
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- package/test-files/import-samples/attributes.graphml +0 -40
- package/test-files/import-samples/port.graphml +0 -32
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