grnsight 4.0.0 → 6.0.0

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Files changed (458) hide show
  1. package/.travis.yml +3 -1
  2. package/GRNsight - Beta.html +194 -0
  3. package/Gemfile.lock +259 -0
  4. package/README.md +2 -2
  5. package/_gh_pages/about.html +360 -45
  6. package/_gh_pages/assets/css/footer.css +3 -0
  7. package/_gh_pages/assets/css/main.css +28 -14
  8. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary-no-targetless-genes_sif.png +0 -0
  9. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary_sif.png +0 -0
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  14. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary-no-targetless-genes_sif.png +0 -0
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  16. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated-no-targetless-genes_sif.png +0 -0
  17. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated_sif.png +0 -0
  18. package/_gh_pages/assets/images/Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
  19. package/_gh_pages/assets/images/Choe_SCCUR_2017.jpg +0 -0
  20. package/_gh_pages/assets/images/Dahlquist-Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
  21. package/_gh_pages/assets/images/Dionisio-Dahlquist_GRNsight-shades_20170506.jpg +0 -0
  22. package/_gh_pages/assets/images/Klein_Samdarshi_TriBeta_2018_20180317.jpg +0 -0
  23. package/_gh_pages/assets/images/Shin_SCCUR_2017.jpg +0 -0
  24. package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure1_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-3_network-sheet.png} +0 -0
  25. package/{documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure2_zoom145_900pix-wide.png → _gh_pages/assets/images/demo-4_network-optimized-weights-sheet.png} +0 -0
  26. package/_gh_pages/assets/images/gene-pages-0.png +0 -0
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  30. package/_gh_pages/assets/images/grnsight2020.png +0 -0
  31. package/_gh_pages/assets/images/v3demo2-grid+nodecoloring.png +0 -0
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  34. package/_gh_pages/assets/js/ga-report.js +11 -11
  35. package/_gh_pages/assets/js/iframeResizer.min.js +9 -0
  36. package/_gh_pages/assets/js/main.js +43 -43
  37. package/_gh_pages/beta.html +29 -24
  38. package/_gh_pages/contact.html +31 -31
  39. package/_gh_pages/coverage/coverage.json +1 -0
  40. package/_gh_pages/coverage/coverage.raw.json +1 -0
  41. package/_gh_pages/coverage/lcov-report/base.css +223 -0
  42. package/_gh_pages/coverage/lcov-report/block-navigation.js +63 -0
  43. package/_gh_pages/coverage/lcov-report/controllers/additional-sheet-parser.js.html +330 -0
  44. package/_gh_pages/coverage/lcov-report/controllers/constants.js.html +243 -0
  45. package/_gh_pages/coverage/lcov-report/controllers/export-controller.js.html +285 -0
  46. package/_gh_pages/coverage/lcov-report/controllers/exporters/graphml.js.html +405 -0
  47. package/_gh_pages/coverage/lcov-report/controllers/exporters/index.html +110 -0
  48. package/_gh_pages/coverage/lcov-report/controllers/exporters/sif.js.html +150 -0
  49. package/_gh_pages/coverage/lcov-report/controllers/helpers.js.html +114 -0
  50. package/_gh_pages/coverage/lcov-report/controllers/import-controller.js.html +233 -0
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  53. package/_gh_pages/coverage/lcov-report/controllers/importers/sif.js.html +488 -0
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  55. package/_gh_pages/coverage/lcov-report/controllers/semantic-checker.js.html +810 -0
  56. package/_gh_pages/coverage/lcov-report/controllers/spreadsheet-controller.js.html +1779 -0
  57. package/_gh_pages/coverage/lcov-report/index.html +136 -0
  58. package/_gh_pages/coverage/lcov-report/prettify.css +1 -0
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  60. package/_gh_pages/coverage/lcov-report/server/controllers/additional-sheet-parser.js.html +330 -0
  61. package/_gh_pages/coverage/lcov-report/server/controllers/constants.js.html +243 -0
  62. package/_gh_pages/coverage/lcov-report/server/controllers/export-controller.js.html +285 -0
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  73. package/_gh_pages/coverage/lcov-report/server/controllers/semantic-checker.js.html +810 -0
  74. package/_gh_pages/coverage/lcov-report/server/controllers/spreadsheet-controller.js.html +1779 -0
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  77. package/_gh_pages/coverage/lcov-report/web-client/public/js/grnstate.js.html +225 -0
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  79. package/_gh_pages/coverage/lcov.info +49 -0
  80. package/_gh_pages/documentation.html +998 -320
  81. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.aux +47 -0
  82. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.bbl +73 -0
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  85. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.out +7 -0
  86. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.synctex.gz +0 -0
  87. package/_gh_pages/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised-Dondi.docx +0 -0
  88. package/_gh_pages/encryption/server.cert +21 -0
  89. package/_gh_pages/encryption/server.key +28 -0
  90. package/_gh_pages/favicon.ico +0 -0
  91. package/_gh_pages/index.html +45 -22
  92. package/_gh_pages/links.html +47 -28
  93. package/_gh_pages/news.html +103 -21
  94. package/_gh_pages/onlyfooter.html +78 -0
  95. package/_gh_pages/onlyheader.html +64 -0
  96. package/_gh_pages/onlysidebar.html +73 -0
  97. package/_gh_pages/package-lock.json +14048 -0
  98. package/_gh_pages/people.html +129 -40
  99. package/_gh_pages/privacy.html +23 -17
  100. package/_gh_pages/publications.html +75 -33
  101. package/_gh_pages/robots.txt +1 -0
  102. package/_gh_pages/sitemap.xml +87 -74
  103. package/_gh_pages/test-files/import-samples/attributes.graphml +40 -0
  104. package/_gh_pages/test-files/import-samples/port.graphml +32 -0
  105. package/_gh_pages/test-files/import-samples/simple.graphml +31 -0
  106. package/_gh_pages/web-client/public/js/grnsight.min.js +2347 -0
  107. package/_gh_pages/web-client/public/stylesheets/grnsight.css +443 -0
  108. package/coverage/coverage.json +1 -1
  109. package/coverage/lcov.info +1847 -1142
  110. package/database/README.md +1 -0
  111. package/database/network-database/README.md +44 -0
  112. package/database/network-database/schema.sql +24 -0
  113. package/database/network-database/scripts/filter_genes.py +76 -0
  114. package/database/network-database/scripts/generate_network.py +199 -0
  115. package/database/network-database/scripts/generate_sgd_network_from_yeastract_network.py +120 -0
  116. package/database/network-database/scripts/loader.py +78 -0
  117. package/package.json +20 -11
  118. package/server/app.js +7 -2
  119. package/server/config/config.js +12 -3
  120. package/server/controllers/additional-sheet-parser.js +292 -55
  121. package/server/controllers/constants.js +4 -37
  122. package/server/controllers/custom-workbook-controller.js +66 -0
  123. package/server/controllers/demo-workbooks.js +5973 -0
  124. package/server/controllers/export-constants.js +78 -0
  125. package/server/controllers/export-controller.js +4 -3
  126. package/server/controllers/exporters/graphml.js +15 -15
  127. package/server/controllers/exporters/sif.js +7 -7
  128. package/server/controllers/exporters/xlsx.js +110 -34
  129. package/server/controllers/expression-database-controller.js +19 -0
  130. package/server/controllers/expression-sheet-parser.js +170 -0
  131. package/server/controllers/graphml-constants.js +0 -17
  132. package/server/controllers/helpers.js +25 -1
  133. package/server/controllers/import-controller.js +2 -2
  134. package/server/controllers/importers/graphml.js +17 -20
  135. package/server/controllers/importers/sif.js +22 -18
  136. package/server/controllers/network-database-controller.js +18 -0
  137. package/server/controllers/network-sheet-parser.js +307 -0
  138. package/server/controllers/semantic-checker.js +30 -162
  139. package/server/controllers/sif-constants.js +36 -0
  140. package/server/controllers/spreadsheet-controller.js +277 -425
  141. package/server/controllers/workbook-constants.js +521 -0
  142. package/server/dals/expression-dal.js +122 -0
  143. package/server/dals/network-dal.js +96 -0
  144. package/test/additional-sheet-parser-tests.js +147 -38
  145. package/test/api-tests.js +3 -6
  146. package/test/errors-adjacency-matrix-modifications.js +30 -29
  147. package/test/errors-graph-tests.js +4 -4
  148. package/test/errors-sheet-modifications.js +10 -2
  149. package/test/export-tests.js +187 -60
  150. package/test/expression-data-import-tests.js +113 -0
  151. package/test/grnstate-tests.js +8 -2
  152. package/test/import-graphml-tests.js +59 -40
  153. package/test/import-sif-tests.js +50 -37
  154. package/test/test.js +554 -91
  155. package/test/warnings-adjacency-matrix-modifications.js +8 -7
  156. package/test-files/additional-sheet-test-files/optimization-diagnostics-default.xlsx +0 -0
  157. package/test-files/additional-sheet-test-files/optimization-diagnostics-extraneous-data.xlsx +0 -0
  158. package/test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-gene-header.xlsx +0 -0
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  163. package/test-files/additional-sheet-test-files/optimization-diagnostics-missing-MSE-data.xlsx +0 -0
  164. package/test-files/additional-sheet-test-files/optimization-diagnostics-missing-column-headers.xlsx +0 -0
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  166. package/test-files/additional-sheet-test-files/optimization-diagnostics-unknown-parameter.xlsx +0 -0
  167. package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
  168. package/test-files/additional-sheet-test-files/optimization-parameters-incorrect-headers.xlsx +0 -0
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  170. package/test-files/additional-sheet-test-files/optimization-parameters-missing-headers.xlsx +0 -0
  171. package/test-files/additional-sheet-test-files/optimization-parameters-unknown-parameter.xlsx +0 -0
  172. package/test-files/additional-sheet-test-files/two-column-sheets-extraneous-data.xlsx +0 -0
  173. package/test-files/additional-sheet-test-files/two-column-sheets-incorrect-cell-A1.xlsx +0 -0
  174. package/test-files/additional-sheet-test-files/two-column-sheets-incorrect-column-header.xlsx +0 -0
  175. package/test-files/additional-sheet-test-files/two-column-sheets-invalid-gene-length.xlsx +0 -0
  176. package/test-files/additional-sheet-test-files/two-column-sheets-invalid-gene-type.xlsx +0 -0
  177. package/test-files/additional-sheet-test-files/two-column-sheets-invalid-value.xlsx +0 -0
  178. package/test-files/additional-sheet-test-files/two-column-sheets-missing-column-header.xlsx +0 -0
  179. package/test-files/additional-sheet-test-files/two-column-sheets-special-character.xlsx +0 -0
  180. package/test-files/adjacency-matrix-modifications/asymmetric-gene-order-input.xlsx +0 -0
  181. package/test-files/adjacency-matrix-modifications/asymmetric-gene-order-output.xlsx +0 -0
  182. package/test-files/adjacency-matrix-modifications/extra-column-adjacent-input.xlsx +0 -0
  183. package/test-files/adjacency-matrix-modifications/extra-column-adjacent-output.xlsx +0 -0
  184. package/test-files/adjacency-matrix-modifications/extra-column-end-of-sheet-input.xlsx +0 -0
  185. package/test-files/adjacency-matrix-modifications/extra-column-end-of-sheet-output.xlsx +0 -0
  186. package/test-files/adjacency-matrix-modifications/extra-data-random-cell-both-output.xlsx +0 -0
  187. package/test-files/adjacency-matrix-modifications/extra-data-random-cell-network-only-input.xlsx +0 -0
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  189. package/test-files/adjacency-matrix-modifications/extra-data-random-cell-network-optimized-only-output.xlsx +0 -0
  190. package/test-files/adjacency-matrix-modifications/extra-row-end-of-sheet-input.xlsx +0 -0
  191. package/test-files/adjacency-matrix-modifications/extra-row-end-of-sheet-output.xlsx +0 -0
  192. package/test-files/adjacency-matrix-modifications/incorrect-network-cell-A1.xlsx +0 -0
  193. package/test-files/adjacency-matrix-modifications/missing-column-end-input.xlsx +0 -0
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  196. package/test-files/adjacency-matrix-modifications/missing-data-output.xlsx +0 -0
  197. package/test-files/adjacency-matrix-modifications/missing-row-end-input.xlsx +0 -0
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  199. package/test-files/adjacency-matrix-modifications/missing-row-middle-input.xlsx +0 -0
  200. package/test-files/adjacency-matrix-modifications/missing-row-middle-output.xlsx +0 -0
  201. package/test-files/adjacency-matrix-modifications/missing-value-bottom-corner-input.xlsx +0 -0
  202. package/test-files/adjacency-matrix-modifications/missing-value-bottom-corner-output.xlsx +0 -0
  203. package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-both-output.xlsx +0 -0
  204. package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-net-only-input.xlsx +0 -0
  205. package/test-files/adjacency-matrix-modifications/value-replaced-w-spaces-net-op-only-output.xlsx +0 -0
  206. package/test-files/adjacency-matrix-modifications/value-replaced/342/200/223w-spaces-net-only-output.xlsx +0 -0
  207. package/test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_estimation_output.xlsx +0 -0
  208. package/test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_input.xlsx +0 -0
  209. package/test-files/expression-data-test-sheets/expression_sheet_correct_numbering.xlsx +0 -0
  210. package/test-files/expression-data-test-sheets/expression_sheet_different_number_of_columns.xlsx +0 -0
  211. package/test-files/expression-data-test-sheets/expression_sheet_empty_column.xlsx +0 -0
  212. package/test-files/expression-data-test-sheets/expression_sheet_empty_row.xlsx +0 -0
  213. package/test-files/expression-data-test-sheets/expression_sheet_erroneous_data.xlsx +0 -0
  214. package/test-files/expression-data-test-sheets/expression_sheet_extra_gene_name.xlsx +0 -0
  215. package/test-files/expression-data-test-sheets/expression_sheet_incorrectly_ordered_time_points.xlsx +0 -0
  216. package/test-files/expression-data-test-sheets/expression_sheet_mismatched_case_gene_names.xlsx +0 -0
  217. package/test-files/expression-data-test-sheets/expression_sheet_mismatched_gene_names.xlsx +0 -0
  218. package/test-files/expression-data-test-sheets/expression_sheet_missing_column_header.xlsx +0 -0
  219. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_error.xlsx +0 -0
  220. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok.xlsx +0 -0
  221. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  222. package/test-files/expression-data-test-sheets/expression_sheet_missing_gene_name.xlsx +0 -0
  223. package/test-files/expression-data-test-sheets/expression_sheet_name_not_in_optparams.xlsx +0 -0
  224. package/test-files/expression-data-test-sheets/expression_sheet_name_not_present.xlsx +0 -0
  225. package/test-files/expression-data-test-sheets/expression_sheet_negative_time_points.xlsx +0 -0
  226. package/test-files/expression-data-test-sheets/expression_sheet_non_numerical_time_points.xlsx +0 -0
  227. package/test-files/expression-data-test-sheets/expression_sheet_not_existing.xlsx +0 -0
  228. package/test-files/expression-data-test-sheets/expression_sheet_wrong_id_label.xlsx +0 -0
  229. package/test-files/expression-data-test-sheets/expression_sheet_wrong_order_gene_names.xlsx +0 -0
  230. package/test-files/expression-data-test-sheets/expression_sheet_wrong_sheet_name_case.xlsx +0 -0
  231. package/test-files/expression-data-test-sheets/expression_sheet_wrong_sheet_name_convention.xlsx +0 -0
  232. package/test-files/gene-name-modifications/NaN-as-gene-name-input.xlsx +0 -0
  233. package/test-files/gene-name-modifications/NaN-as-gene-name-output.xlsx +0 -0
  234. package/test-files/gene-name-modifications/mismatched-case-related-input.xlsx +0 -0
  235. package/test-files/gene-name-modifications/mismatched-case-related-output.xlsx +0 -0
  236. package/test-files/gene-name-modifications/mismatched-case-unrelated-input.xlsx +0 -0
  237. package/test-files/gene-name-modifications/mismatched-case-unrelated-output.xlsx +0 -0
  238. package/test-files/graph-tests/different-sized-networks/{80-genes-0-edges.xlsx → 134-genes-0-edges.xlsx} +0 -0
  239. package/test-files/graph-tests/different-sized-networks/{45-genes-max-edges.xlsx → 44-source-genes-45-target-genes-max-edges.xlsx} +0 -0
  240. package/test-files/graph-tests/different-sized-networks/{1-gene-0-edges.xlsx → unused-files/1-gene-0-edges.xlsx} +0 -0
  241. package/test-files/graph-tests/different-sized-networks/{1-gene-1-edges.xlsx → unused-files/1-gene-1-edges.xlsx} +0 -0
  242. package/test-files/graph-tests/different-sized-networks/{10-genes-50-edges.xlsx → unused-files/10-genes-50-edges.xlsx} +0 -0
  243. package/test-files/graph-tests/different-sized-networks/{10-genes-90-edges.xlsx → unused-files/10-genes-90-edges.xlsx} +0 -0
  244. package/test-files/graph-tests/different-sized-networks/{100-genes-0-edges.xlsx → unused-files/100-genes-0-edges.xlsx} +0 -0
  245. package/test-files/graph-tests/different-sized-networks/{110-genes-0-edges.xlsx → unused-files/110-genes-0-edges.xlsx} +0 -0
  246. package/test-files/graph-tests/different-sized-networks/{120-genes-0-edges.xlsx → unused-files/120-genes-0-edges.xlsx} +0 -0
  247. package/test-files/graph-tests/different-sized-networks/{130-genes-0-edges.xlsx → unused-files/130-genes-0-edges.xlsx} +0 -0
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