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.
- package/.eslintrc.yml +4 -4
- package/database/README.md +224 -79
- package/database/constants.py +42 -0
- 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/filter_update.py +168 -0
- package/database/grnsettings-database/README.md +52 -0
- package/database/grnsettings-database/schema.sql +4 -0
- package/database/loader.py +30 -0
- package/database/loader_update.py +36 -0
- package/database/network-database/README.md +36 -4
- package/database/network-database/schema.sql +7 -7
- package/database/network-database/scripts/generate_network.py +16 -24
- package/database/network-database/scripts/generate_new_network_version.py +216 -0
- package/database/protein-protein-database/README.md +71 -0
- package/database/protein-protein-database/schema.sql +37 -0
- package/database/protein-protein-database/scripts/generate_protein_network.py +227 -0
- package/database/protein-protein-database/scripts/remove_duplicates.sh +4 -0
- package/database/utils.py +418 -0
- package/package.json +2 -2
- package/server/app.js +2 -0
- package/server/config/config.js +4 -4
- package/server/controllers/additional-sheet-parser.js +2 -1
- package/server/controllers/constants.js +5 -0
- package/server/controllers/custom-workbook-controller.js +8 -6
- package/server/controllers/demo-workbooks.js +1460 -4
- package/server/controllers/export-constants.js +3 -2
- package/server/controllers/exporters/sif.js +6 -1
- package/server/controllers/exporters/xlsx.js +8 -3
- package/server/controllers/expression-sheet-parser.js +0 -6
- package/server/controllers/grnsettings-database-controller.js +17 -0
- package/server/controllers/importers/sif.js +29 -11
- package/server/controllers/network-database-controller.js +2 -2
- package/server/controllers/network-sheet-parser.js +54 -12
- package/server/controllers/protein-database-controller.js +18 -0
- package/server/controllers/sif-constants.js +4 -4
- package/server/controllers/spreadsheet-controller.js +44 -1
- package/server/controllers/workbook-constants.js +21 -4
- package/server/dals/expression-dal.js +8 -7
- package/server/dals/grnsetting-dal.js +49 -0
- package/server/dals/network-dal.js +13 -12
- package/server/dals/protein-dal.js +106 -0
- package/test/export-tests.js +136 -9
- package/test/import-sif-tests.js +54 -13
- package/test/test.js +1 -1
- package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
- package/test-files/demo-files/18_proteins_81_edges_PPI.xlsx +0 -0
- package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
- package/web-client/config/config.js +4 -4
- package/web-client/public/js/api/grnsight-api.js +72 -56
- package/web-client/public/js/constants.js +26 -12
- package/web-client/public/js/generateNetwork.js +173 -67
- package/web-client/public/js/graph.js +420 -150
- package/web-client/public/js/grnsight.js +25 -4
- package/web-client/public/js/grnstate.js +3 -1
- package/web-client/public/js/iframe-coordination.js +3 -3
- package/web-client/public/js/setup-handlers.js +28 -32
- package/web-client/public/js/setup-load-and-import-handlers.js +196 -170
- package/web-client/public/js/update-app.js +84 -17
- package/web-client/public/js/upload.js +193 -157
- package/web-client/public/lib/bootstrap.file-input/bootstrap.file-input.js +0 -1
- package/web-client/public/stylesheets/grnsight.styl +40 -16
- package/web-client/views/components/demo.pug +7 -5
- package/web-client/views/upload.pug +63 -49
- 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
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- 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
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- package/_gh_pages/coverage/lcov-report/server/controllers/importers/sif.js.html +0 -492
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- 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
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- 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
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- package/_gh_pages/onlyheader.html +0 -64
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