grnsight 4.0.0 → 6.0.0

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 (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
  10. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_3-edges-and-footer.png +0 -0
  11. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_header-and-3-nodes.png +0 -0
  12. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_output_3-edges-and-footer.png +0 -0
  13. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_output_header-and-3-nodes.png +0 -0
  14. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary-no-targetless-genes_sif.png +0 -0
  15. package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary_sif.png +0 -0
  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
  27. package/_gh_pages/assets/images/gene-pages-1.png +0 -0
  28. package/_gh_pages/assets/images/gene-pages-2.png +0 -0
  29. package/_gh_pages/assets/images/gene-pages-3.png +0 -0
  30. package/_gh_pages/assets/images/grnsight2020.png +0 -0
  31. package/_gh_pages/assets/images/v3demo2-grid+nodecoloring.png +0 -0
  32. package/_gh_pages/assets/images/v3demo2-nodecoloring.png +0 -0
  33. package/_gh_pages/assets/images/v3demo2.png +0 -0
  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
  51. package/_gh_pages/coverage/lcov-report/controllers/importers/graphml.js.html +716 -0
  52. package/_gh_pages/coverage/lcov-report/controllers/importers/index.html +106 -0
  53. package/_gh_pages/coverage/lcov-report/controllers/importers/sif.js.html +488 -0
  54. package/_gh_pages/coverage/lcov-report/controllers/index.html +162 -0
  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
  59. package/_gh_pages/coverage/lcov-report/prettify.js +1 -0
  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
  63. package/_gh_pages/coverage/lcov-report/server/controllers/exporters/graphml.js.html +405 -0
  64. package/_gh_pages/coverage/lcov-report/server/controllers/exporters/index.html +110 -0
  65. package/_gh_pages/coverage/lcov-report/server/controllers/exporters/sif.js.html +150 -0
  66. package/_gh_pages/coverage/lcov-report/server/controllers/graphml-constants.js.html +585 -0
  67. package/_gh_pages/coverage/lcov-report/server/controllers/helpers.js.html +114 -0
  68. package/_gh_pages/coverage/lcov-report/server/controllers/import-controller.js.html +237 -0
  69. package/_gh_pages/coverage/lcov-report/server/controllers/importers/graphml.js.html +585 -0
  70. package/_gh_pages/coverage/lcov-report/server/controllers/importers/index.html +110 -0
  71. package/_gh_pages/coverage/lcov-report/server/controllers/importers/sif.js.html +492 -0
  72. package/_gh_pages/coverage/lcov-report/server/controllers/index.html +188 -0
  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
  75. package/_gh_pages/coverage/lcov-report/sort-arrow-sprite.png +0 -0
  76. package/_gh_pages/coverage/lcov-report/sorter.js +158 -0
  77. package/_gh_pages/coverage/lcov-report/web-client/public/js/grnstate.js.html +225 -0
  78. package/_gh_pages/coverage/lcov-report/web-client/public/js/index.html +97 -0
  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
  83. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.blg +52 -0
  84. package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.log +1056 -0
  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
  159. package/test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-header.xlsx +0 -0
  160. package/test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-column-headers.xlsx +0 -0
  161. package/test-files/additional-sheet-test-files/optimization-diagnostics-invalid-MSE-data.xlsx +0 -0
  162. package/test-files/additional-sheet-test-files/optimization-diagnostics-invalid-value.xlsx +0 -0
  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
  165. package/test-files/additional-sheet-test-files/optimization-diagnostics-missing-header.xlsx +0 -0
  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
  169. package/test-files/additional-sheet-test-files/optimization-parameters-invalid-optimization-parameter.xlsx +0 -0
  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
  188. package/test-files/adjacency-matrix-modifications/extra-data-random-cell-network-only-output.xlsx +0 -0
  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
  194. package/test-files/adjacency-matrix-modifications/missing-column-end-output.xlsx +0 -0
  195. package/test-files/adjacency-matrix-modifications/missing-data-input.xlsx +0 -0
  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
  198. package/test-files/adjacency-matrix-modifications/missing-row-end-output.xlsx +0 -0
  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
  248. package/test-files/graph-tests/different-sized-networks/{140-genes-0-edges.xlsx → unused-files/140-genes-0-edges.xlsx} +0 -0
  249. package/test-files/graph-tests/different-sized-networks/{150-genes-10000-edges.xlsx → unused-files/150-genes-10000-edges.xlsx} +0 -0
  250. package/test-files/graph-tests/different-sized-networks/{150-genes-20000-edges.xlsx → unused-files/150-genes-20000-edges.xlsx} +0 -0
  251. package/test-files/graph-tests/different-sized-networks/{150-genes-max-edges.xlsx → unused-files/150-genes-max-edges.xlsx} +0 -0
  252. package/test-files/graph-tests/different-sized-networks/{160-genes-max-edges.xlsx → unused-files/160-genes-max-edges.xlsx} +0 -0
  253. package/test-files/graph-tests/different-sized-networks/{20-genes-max-edges.xlsx → unused-files/20-genes-max-edges.xlsx} +0 -0
  254. package/test-files/graph-tests/different-sized-networks/{25-genes-max-edges.xlsx → unused-files/25-genes-max-edges.xlsx} +0 -0
  255. package/test-files/graph-tests/different-sized-networks/{30-genes-max-edges.xlsx → unused-files/30-genes-max-edges.xlsx} +0 -0
  256. package/test-files/graph-tests/different-sized-networks/{34-genes-0-edges.xlsx → unused-files/34-genes-0-edges.xlsx} +0 -0
  257. package/test-files/graph-tests/different-sized-networks/{34-genes-40-edges.xlsx → unused-files/34-genes-40-edges.xlsx} +0 -0
  258. package/test-files/graph-tests/different-sized-networks/{34-genes-65-edges.xlsx → unused-files/34-genes-65-edges.xlsx} +0 -0
  259. package/test-files/graph-tests/different-sized-networks/{34-genes-90-edges.xlsx → unused-files/34-genes-90-edges.xlsx} +0 -0
  260. package/test-files/graph-tests/different-sized-networks/{5-genes-max-edges.xlsx → unused-files/5-genes-max-edges.xlsx} +0 -0
  261. package/test-files/graph-tests/different-sized-networks/{51-genes-max-edges.xlsx → unused-files/51-genes-max-edges.xlsx} +0 -0
  262. package/test-files/graph-tests/different-sized-networks/{52-genes-max-edges.xlsx → unused-files/52-genes-max-edges.xlsx} +0 -0
  263. package/test-files/graph-tests/different-sized-networks/{55-genes-0-edges.xlsx → unused-files/55-genes-0-edges.xlsx} +0 -0
  264. package/test-files/graph-tests/different-sized-networks/{55-genes-max-edges.xlsx → unused-files/55-genes-max-edges.xlsx} +0 -0
  265. package/test-files/graph-tests/different-sized-networks/{65-genes-0-edges.xlsx → unused-files/65-genes-0-edges.xlsx} +0 -0
  266. package/test-files/graph-tests/different-sized-networks/{7-genes-max-edges.xlsx → unused-files/7-genes-max-edges.xlsx} +0 -0
  267. package/test-files/graph-tests/different-sized-networks/{70-genes-0-edges.xlsx → unused-files/70-genes-0-edges.xlsx} +0 -0
  268. package/test-files/graph-tests/different-sized-networks/{9-genes-max-edges.xlsx → unused-files/9-genes-max-edges.xlsx} +0 -0
  269. package/test-files/graph-tests/different-sized-networks/{90-genes-0-edges.xlsx → unused-files/90-genes-0-edges.xlsx} +0 -0
  270. package/test-files/graph-tests/different-sized-networks/{regulation-matrix-documented-20140709-AllTF-all-targets.xlsx → unused-files/regulation-matrix-documented-20140709-AllTF-all-targets.xlsx} +0 -0
  271. package/test-files/node-tests/long-gene-name-no-spaces-first.xlsx +0 -0
  272. package/test-files/node-tests/long-gene-name-no-spaces-second.xlsx +0 -0
  273. package/test-files/node-tests/long-gene-name-spaces.xlsx +0 -0
  274. package/test-files/species-test-data/15-genes_28-edges_db5_Dahlquist-data_input_no-species.xlsx +0 -0
  275. package/test-files/species-test-data/15-genes_28-edges_db5_Dahlquist-data_input_with-species.xlsx +0 -0
  276. package/test-files/species-test-data/3-gene_7-edge_elegans.xlsx +0 -0
  277. package/test-files/species-test-data/3-gene_7-edge_melanogaster.xlsx +0 -0
  278. package/test-files/species-test-data/3-gene_7-edge_musculus.xlsx +0 -0
  279. package/test-files/species-test-data/3-gene_7-edge_sapiens.xlsx +0 -0
  280. package/test-files/species-test-data/kev-fake-data-sapiens-no-exp-data.xlsx +0 -0
  281. package/test-files/spreadsheet-controller-test-files/sheet-name-capitalized-network-optimized-weights.xlsx +0 -0
  282. package/test-files/spreadsheet-controller-test-files/sheet-name-capitalized-network.xlsx +0 -0
  283. package/web-client/app.js +1 -1
  284. package/web-client/controllers/main.js +1 -1
  285. package/web-client/public/favicon.ico +0 -0
  286. package/web-client/public/gene/api.js +76 -14
  287. package/web-client/public/gene/info.js +19 -8
  288. package/web-client/public/js/api/grnsight-api.js +124 -0
  289. package/web-client/public/js/constants.js +90 -17
  290. package/web-client/public/js/createNetwork.js +195 -0
  291. package/web-client/public/js/graph-statistics.js +7 -7
  292. package/web-client/public/js/graph.js +369 -324
  293. package/web-client/public/js/grnsight.js +2 -2
  294. package/web-client/public/js/grnsight.min.js +128 -59
  295. package/web-client/public/js/grnstate.js +54 -30
  296. package/web-client/public/js/iframe-coordination.js +55 -0
  297. package/web-client/public/js/setup-handlers.js +358 -18
  298. package/web-client/public/js/setup-load-and-import-handlers.js +105 -66
  299. package/web-client/public/js/update-app.js +483 -93
  300. package/web-client/public/js/upload.js +349 -32
  301. package/web-client/public/js/warnings.js +13 -51
  302. package/web-client/public/lib/iframeSizer.contentWindow.min.js +10 -0
  303. package/web-client/public/stylesheets/grnsight.styl +323 -28
  304. package/web-client/views/components/demo.pug +10 -0
  305. package/web-client/views/{graph.jade → graph.pug} +0 -0
  306. package/web-client/views/{info.jade → info.pug} +1 -5
  307. package/web-client/views/upload.pug +580 -0
  308. package/_gh_pages/Gemfile +0 -7
  309. package/_gh_pages/Gemfile.lock +0 -129
  310. package/documents/SDF/CMSI_402/spring_2014/Southwick_CMSI402_Spring2014_software-development-plan.md +0 -71
  311. package/documents/SDF/CMSI_402/spring_2014/Southwick_CMSI402_Spring2014_software-requirements-specification.md +0 -71
  312. package/documents/SDF/CMSI_402/spring_2014/use-case-diagram-spring-2014.jpg +0 -0
  313. package/documents/SDF/CMSI_402/spring_2017/Anguiano_402_Final_Presentation.pptx +0 -0
  314. package/documents/SDF/CMSI_402/spring_2017/Anguiano_402_Presentation_Final_Poster.pdf +0 -0
  315. package/documents/SDF/CMSI_402/spring_2017/Anguiano_CMSI402_Spring2017_project-proposal-presentation.pptx +0 -0
  316. package/documents/SDF/CMSI_402/spring_2017/Anguiano_CMSI402_Spring2017_project-proposal.docx +0 -0
  317. package/documents/SDF/CMSI_402/spring_2017/Anguiano_CMSI402_Spring2017_software-development-plan.docx +0 -0
  318. package/documents/SDF/CMSI_402/spring_2017/Anguiano_CMSI402_Spring2017_software-requirements-specification.docx +0 -0
  319. package/documents/SDF/CMSI_402/spring_2017/Design Review Presentation.pptx +0 -0
  320. package/documents/SDF/CMSI_402/spring_2018/0402report.docx +0 -0
  321. package/documents/SDF/CMSI_402/spring_2018/0409report.docx +0 -0
  322. package/documents/SDF/CMSI_402/spring_2018/402-gantt.png +0 -0
  323. package/documents/SDF/CMSI_402/spring_2018/402SRS_GRNSightFeedback01.txt +0 -28
  324. package/documents/SDF/CMSI_402/spring_2018/402_SPD.md +0 -223
  325. package/documents/SDF/CMSI_402/spring_2018/ChoeShinCMSI402_Final.pptx +0 -0
  326. package/documents/SDF/CMSI_402/spring_2018/ProjectProposal.md +0 -22
  327. package/documents/SDF/CMSI_402/spring_2018/SoftwareRequirementsSpecification.md +0 -88
  328. package/documents/SDF/CMSI_402/spring_2018/homework/choe_eileen/Choe_Eileen_CMSI 402_HW1.pdf +0 -0
  329. package/documents/SDF/CMSI_402/spring_2018/homework/choe_eileen/Choe_Eileen_CMSI402_HW2.pdf +0 -0
  330. package/documents/SDF/CMSI_402/spring_2018/homework/shin_jen/402hw2.docx +0 -0
  331. package/documents/SDF/CMSI_402/spring_2018/homework/shin_jen/Jen - 402Hw1.docx +0 -0
  332. package/documents/SDF/CMSI_402/spring_2018/homework/shin_jen/Jen - hw3.docx +0 -0
  333. package/documents/SDF/CMSI_402/spring_2018/writtenStatusReport.docx +0 -0
  334. package/documents/SDF/CMSI_402/spring_2018/writtenStatusReport4 +0 -0
  335. package/documents/abstracts/Anguiano_Varshneya_Undergraduate-Research-Symposium_2017_abstract.pdf +0 -0
  336. package/documents/abstracts/SIGGRAPH 2017 Abstract/ACM-Reference-Format.bst +0 -3478
  337. package/documents/abstracts/SIGGRAPH 2017 Abstract/Figure1_zoom100.png +0 -0
  338. package/documents/abstracts/SIGGRAPH 2017 Abstract/acmart.cls +0 -2352
  339. package/documents/abstracts/SIGGRAPH 2017 Abstract/acmart.ins +0 -29
  340. package/documents/abstracts/SIGGRAPH 2017 Abstract/always-weights.png +0 -0
  341. package/documents/abstracts/SIGGRAPH 2017 Abstract/auto.png +0 -0
  342. package/documents/abstracts/SIGGRAPH 2017 Abstract/networkA.png +0 -0
  343. package/documents/abstracts/SIGGRAPH 2017 Abstract/networkB-normalized.png +0 -0
  344. package/documents/abstracts/SIGGRAPH 2017 Abstract/networkB.png +0 -0
  345. package/documents/abstracts/SIGGRAPH 2017 Abstract/never-weights.png +0 -0
  346. package/documents/abstracts/SIGGRAPH 2017 Abstract/representative-image/screenshot.jpg +0 -0
  347. package/documents/abstracts/SIGGRAPH 2017 Abstract/representative-image/screenshot3x2.png +0 -0
  348. package/documents/abstracts/SIGGRAPH 2017 Abstract/representative-image/withweights3x2.png +0 -0
  349. package/documents/abstracts/SIGGRAPH 2017 Abstract/screenshot-auto.png +0 -0
  350. package/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.bib +0 -85
  351. package/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.pdf +0 -0
  352. package/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.tex +0 -235
  353. package/documents/abstracts/SWE Collegiate Competition 2017.md +0 -9
  354. package/documents/abstracts/Samdarshi_GRNsight_SoCalSysBio_Abstract_2019.docx +0 -0
  355. package/documents/abstracts/Varshneya_Samdarshi_Southern-California-Systems-Biology_2017_abstract.docx +0 -0
  356. package/documents/abstracts/~$mdarshi_SoCalSysBio_Abstract_2019.docx +0 -0
  357. package/documents/developer_documents/State Diagram.graphml +0 -3525
  358. package/documents/developer_documents/graphml/State Diagram.graphml +0 -3115
  359. package/documents/developer_documents/older_versions/GRNsight State Diagram old.png +0 -0
  360. package/documents/developer_documents/older_versions/GRNsight State Diagram.png +0 -0
  361. package/documents/developer_documents/testing_script_generator/GRNsightTestingDocument.md +0 -998
  362. package/documents/developer_documents/testing_script_generator/featureList.json +0 -496
  363. package/documents/developer_documents/testing_script_generator/testing-script-generator.js +0 -149
  364. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_conference-presentations_2016.docx +0 -0
  365. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016.docx +0 -0
  366. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016_Table1.docx +0 -0
  367. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016_references.rtf +0 -264
  368. package/documents/manuscripts/peerj-computerscience-2016/GRNsight_PeerJ-CS_manuscript_2016_text-only.docx +0 -0
  369. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/21-genes_31-edges_Schade-data_for-screenshots.xlsx +0 -0
  370. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure1_zoom100.jpg +0 -0
  371. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure1_zoom100.png +0 -0
  372. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure1_zoom100.psd +0 -0
  373. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure1_zoom145.jpg +0 -0
  374. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure1_zoom145.png +0 -0
  375. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure1_zoom145.psd +0 -0
  376. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure1_zoom145_900pix-wide.psd +0 -0
  377. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure2_zoom100.jpg +0 -0
  378. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure2_zoom100.png +0 -0
  379. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure2_zoom100.psd +0 -0
  380. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure2_zoom145.jpg +0 -0
  381. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure2_zoom145.png +0 -0
  382. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure2_zoom145.psd +0 -0
  383. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure2_zoom145_900pix-wide.psd +0 -0
  384. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5A.pdf +0 -0
  385. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5B.pdf +0 -0
  386. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5C.eps +0 -0
  387. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5D.pdf +0 -0
  388. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5E.pdf +0 -0
  389. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5F.eps +0 -0
  390. package/documents/manuscripts/peerj-computerscience-2016/figures/other-versions/Figure5_compiled.png +0 -0
  391. package/documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure3_GRNsight-Architecture.pdf +0 -0
  392. package/documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure4_GRNsight-Screenshot.pdf +0 -0
  393. package/documents/manuscripts/peerj-computerscience-2016/figures/submitted-versions/Figure5_compiled.pdf +12 -5383
  394. package/documents/manuscripts/peerj-computerscience-2016/peerj-reviewing-10823-v0.pdf +0 -0
  395. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_conference-presentations_2016_revised.docx +0 -0
  396. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_cover-letter-and-response_2016.pdf +0 -0
  397. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_cover-letter_2016.docx +0 -0
  398. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_cover-letter_2016.pdf +0 -0
  399. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_Table1.docx +0 -0
  400. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_references_revised.rtf +0 -385
  401. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised.docx +0 -0
  402. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised_marked.docx +0 -0
  403. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_response-to-reviewers_2016.docx +0 -0
  404. package/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_response-to-reviewers_2016.pdf +0 -0
  405. package/documents/manuscripts/peerj-computerscience-2016/revisions/figures/Figure3_GRNsight-Architecture.pdf +0 -0
  406. package/documents/manuscripts/peerj-computerscience-2016/revisions/figures/Figure4_GRNsight-Screenshot-auto.pdf +0 -0
  407. package/documents/manuscripts/peerj-computerscience-2016/revisions/figures/Figure4_GRNsight-Screenshot.pdf +0 -0
  408. package/documents/manuscripts/peerj-computerscience-2016/revisions/peerj-reviewing-10823-v1.pdf +0 -0
  409. package/documents/posters/Anguiano_CMSI402_2017.pptx +0 -0
  410. package/documents/posters/Anguiano_Varshneya_LMU-Symposium_2015.pptx +0 -0
  411. package/documents/posters/Anguiano_Varshneya_SCCUR_2014.pptx +0 -0
  412. package/documents/posters/Choe_Shin_CMSI402_2018.pptx +0 -0
  413. package/documents/posters/Dahlquist-et-al_BOSC_ISMB_2016_poster.pptx +0 -0
  414. package/documents/posters/Lopez_Filler_LMU_Symposium_2019.pdf +0 -0
  415. package/documents/posters/Lopez_Filler_LMU_Symposium_2019.pptx +0 -0
  416. package/documents/posters/Samdarshi-et-al_LMU-Symposium_2017.pptx +0 -0
  417. package/documents/posters/Samdarshi-et-al_LMU-Symposium_2018.pptx +0 -0
  418. package/documents/posters/Samdarshi-et-al_SoCalSysBio_2019.pptx +0 -0
  419. package/documents/posters/Shin-et-al_SCCUR_2017.pptx +0 -0
  420. package/documents/posters/Southwick_CMSI402_2014.pptx +0 -0
  421. package/documents/posters/Varshneya_Samdarshi_LMU-Symposium_2016.pptx +0 -0
  422. package/documents/posters/Varshneya_Samdarshi_SoCalSysBio_2017.pptx +0 -0
  423. package/documents/presentations/Anguiano_402_Final_Presentation.pptx +0 -0
  424. package/documents/presentations/Choe_SWERapidFire2017_final.pptx +0 -0
  425. package/documents/presentations/Dahlquist_BOSC_20160709.pptx +0 -0
  426. package/documents/presentations/Dahlquist_ExperimentalBiology_20160404_talk.pptx +0 -0
  427. package/documents/presentations/Dahlquist_SoCalSysBio_20150131_talk.pptx +0 -0
  428. package/documents/presentations/Samdarshi_LMU-Symposium_20190323_talk.pdf +0 -0
  429. package/documents/presentations/Samdarshi_LMU-Symposium_20190323_talk.pptx +0 -0
  430. package/documents/presentations/Southwick_Anguiano_LMU-Symposium_20140329_talk.pptx +0 -0
  431. package/documents/presentations/Southwick_CMSI402_Presentation_20140508_talk.pptx +0 -0
  432. package/documents/presentations/Varshneya_Anguiano_LMU-Symposium_201703_talk.pptx +0 -0
  433. package/documents/reports/Samdarshi_Mihir_2019/Samdarshi_2019_Final.docx +0 -0
  434. package/documents/reports/Samdarshi_Mihir_2019/Samdarshi_Mihir_2019_AnnotatedBibliography.docx +0 -0
  435. package/documents/reports/Samdarshi_Mihir_2019/Samdarshi_Mihir_2019_Outline.docx +0 -0
  436. package/documents/reports/Samdarshi_Mihir_2019/~$mdarshi_2019_Draft.docx +0 -0
  437. package/documents/reports/Samdarshi_Mihir_2019/~$mdarshi_2019_Final_Paper_Draft.docx +0 -0
  438. package/documents/reports/Varshneya_Anu_2017/Varshneya-201701-AnnotatedBibliography.docx +0 -0
  439. package/documents/reports/Varshneya_Anu_2017/Varshneya-201702-Introduction.docx +0 -0
  440. package/documents/reports/Varshneya_Anu_2017/Varshneya-201702-Outline.docx +0 -0
  441. package/documents/reports/Varshneya_Anu_2017/Varshneya-201703-Discussion.docx +0 -0
  442. package/documents/reports/Varshneya_Anu_2017/Varshneya-201703-MMResults.docx +0 -0
  443. package/documents/reports/Varshneya_Anu_2017/Varshneya-201704-Draft-1.docx +0 -0
  444. package/documents/reports/Varshneya_Anu_2017/Varshneya-201704-Final.docx +0 -0
  445. package/onlysidebar.html +0 -8
  446. package/test/graph-library-tests.js +0 -165
  447. package/test-files/demo-files/21-genes_50-edges_Dahlquist-data_estimation_output.xlsx +0 -0
  448. package/test-files/demo-files/21-genes_50-edges_Dahlquist-data_input.xlsx +0 -0
  449. package/test-files/graph-tests/different-sized-networks/10-genes-max-edges.xlsx +0 -0
  450. package/test-files/graph-tests/different-sized-networks/12-genes-max-edges.xlsx +0 -0
  451. package/test-files/graph-tests/different-sized-networks/35-genes-max-edges.xlsx +0 -0
  452. package/test-files/graph-tests/different-sized-networks/40-genes-0-edges.xlsx +0 -0
  453. package/test-files/graph-tests/different-sized-networks/40-genes-max-edges.xlsx +0 -0
  454. package/test-files/graph-tests/different-sized-networks/42-genes-max-edges.xlsx +0 -0
  455. package/test-files/graph-tests/different-sized-networks/50-genes-max-edges.xlsx +0 -0
  456. package/test-files/graph-tests/different-sized-networks/75-genes-150-edges.xlsx +0 -0
  457. package/web-client/public/js/container.js +0 -121
  458. package/web-client/views/upload.jade +0 -464
@@ -0,0 +1,114 @@
1
+ <!doctype html>
2
+ <html lang="en">
3
+ <head>
4
+ <title>Code coverage report for server/controllers/helpers.js</title>
5
+ <meta charset="utf-8" />
6
+ <link rel="stylesheet" href="../../prettify.css" />
7
+ <link rel="stylesheet" href="../../base.css" />
8
+ <meta name="viewport" content="width=device-width, initial-scale=1">
9
+ <style type='text/css'>
10
+ .coverage-summary .sorter {
11
+ background-image: url(../../sort-arrow-sprite.png);
12
+ }
13
+ </style>
14
+ </head>
15
+ <body>
16
+ <div class='wrapper'>
17
+ <div class='pad1'>
18
+ <h1>
19
+ <a href="../../index.html">All files</a> / <a href="index.html">server/controllers</a> helpers.js
20
+ </h1>
21
+ <div class='clearfix'>
22
+ <div class='fl pad1y space-right2'>
23
+ <span class="strong">33.33% </span>
24
+ <span class="quiet">Statements</span>
25
+ <span class='fraction'>2/6</span>
26
+ </div>
27
+ <div class='fl pad1y space-right2'>
28
+ <span class="strong">100% </span>
29
+ <span class="quiet">Branches</span>
30
+ <span class='fraction'>0/0</span>
31
+ </div>
32
+ <div class='fl pad1y space-right2'>
33
+ <span class="strong">0% </span>
34
+ <span class="quiet">Functions</span>
35
+ <span class='fraction'>0/2</span>
36
+ </div>
37
+ <div class='fl pad1y space-right2'>
38
+ <span class="strong">33.33% </span>
39
+ <span class="quiet">Lines</span>
40
+ <span class='fraction'>2/6</span>
41
+ </div>
42
+ </div>
43
+ <p class="quiet">
44
+ Press <em>n</em> or <em>j</em> to go to the next uncovered block, <em>b</em>, <em>p</em> or <em>k</em> for the previous block.
45
+ </p>
46
+ </div>
47
+ <div class='status-line low'></div>
48
+ <pre><table class="coverage">
49
+ <tr><td class="line-count quiet"><a name='L1'></a><a href='#L1'>1</a>
50
+ <a name='L2'></a><a href='#L2'>2</a>
51
+ <a name='L3'></a><a href='#L3'>3</a>
52
+ <a name='L4'></a><a href='#L4'>4</a>
53
+ <a name='L5'></a><a href='#L5'>5</a>
54
+ <a name='L6'></a><a href='#L6'>6</a>
55
+ <a name='L7'></a><a href='#L7'>7</a>
56
+ <a name='L8'></a><a href='#L8'>8</a>
57
+ <a name='L9'></a><a href='#L9'>9</a>
58
+ <a name='L10'></a><a href='#L10'>10</a>
59
+ <a name='L11'></a><a href='#L11'>11</a>
60
+ <a name='L12'></a><a href='#L12'>12</a>
61
+ <a name='L13'></a><a href='#L13'>13</a>
62
+ <a name='L14'></a><a href='#L14'>14</a>
63
+ <a name='L15'></a><a href='#L15'>15</a>
64
+ <a name='L16'></a><a href='#L16'>16</a></td><td class="line-coverage quiet"><span class="cline-any cline-yes">1x</span>
65
+ <span class="cline-any cline-neutral">&nbsp;</span>
66
+ <span class="cline-any cline-yes">1x</span>
67
+ <span class="cline-any cline-neutral">&nbsp;</span>
68
+ <span class="cline-any cline-neutral">&nbsp;</span>
69
+ <span class="cline-any cline-no">&nbsp;</span>
70
+ <span class="cline-any cline-neutral">&nbsp;</span>
71
+ <span class="cline-any cline-neutral">&nbsp;</span>
72
+ <span class="cline-any cline-neutral">&nbsp;</span>
73
+ <span class="cline-any cline-no">&nbsp;</span>
74
+ <span class="cline-any cline-no">&nbsp;</span>
75
+ <span class="cline-any cline-no">&nbsp;</span>
76
+ <span class="cline-any cline-neutral">&nbsp;</span>
77
+ <span class="cline-any cline-neutral">&nbsp;</span>
78
+ <span class="cline-any cline-neutral">&nbsp;</span>
79
+ <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var constants = require(__dirname + "/constants");
80
+ &nbsp;
81
+ module.exports = {
82
+ &nbsp;
83
+ attachCorsHeader: <span class="fstat-no" title="function not covered" >function (</span>res, app) {
84
+ <span class="cstat-no" title="statement not covered" > res.header("Access-Control-Allow-Origin", app.get("corsOrigin"));</span>
85
+ },
86
+ &nbsp;
87
+ attachFileHeaders: <span class="fstat-no" title="function not covered" >function (</span>res, path) {
88
+ <span class="cstat-no" title="statement not covered" > res.header("Access-Control-Allow-Methods", "POST, GET");</span>
89
+ <span class="cstat-no" title="statement not covered" > res.header("Access-Control-Expose-Headers", constants.GRNSIGHT_FILENAME_HEADER);</span>
90
+ <span class="cstat-no" title="statement not covered" > res.header(constants.GRNSIGHT_FILENAME_HEADER, path.split("/").pop());</span>
91
+ }
92
+ &nbsp;
93
+ };
94
+ &nbsp;</pre></td></tr>
95
+ </table></pre>
96
+ <div class='push'></div><!-- for sticky footer -->
97
+ </div><!-- /wrapper -->
98
+ <div class='footer quiet pad2 space-top1 center small'>
99
+ Code coverage
100
+ generated by <a href="https://istanbul.js.org/" target="_blank">istanbul</a> at Thu May 31 2018 15:29:57 GMT-0700 (PDT)
101
+ </div>
102
+ </div>
103
+ <script src="../../prettify.js"></script>
104
+ <script>
105
+ window.onload = function () {
106
+ if (typeof prettyPrint === 'function') {
107
+ prettyPrint();
108
+ }
109
+ };
110
+ </script>
111
+ <script src="../../sorter.js"></script>
112
+ <script src="../../block-navigation.js"></script>
113
+ </body>
114
+ </html>
@@ -0,0 +1,237 @@
1
+ <!doctype html>
2
+ <html lang="en">
3
+ <head>
4
+ <title>Code coverage report for server/controllers/import-controller.js</title>
5
+ <meta charset="utf-8" />
6
+ <link rel="stylesheet" href="../../prettify.css" />
7
+ <link rel="stylesheet" href="../../base.css" />
8
+ <meta name="viewport" content="width=device-width, initial-scale=1">
9
+ <style type='text/css'>
10
+ .coverage-summary .sorter {
11
+ background-image: url(../../sort-arrow-sprite.png);
12
+ }
13
+ </style>
14
+ </head>
15
+ <body>
16
+ <div class='wrapper'>
17
+ <div class='pad1'>
18
+ <h1>
19
+ <a href="../../index.html">All files</a> / <a href="index.html">server/controllers</a> import-controller.js
20
+ </h1>
21
+ <div class='clearfix'>
22
+ <div class='fl pad1y space-right2'>
23
+ <span class="strong">20.69% </span>
24
+ <span class="quiet">Statements</span>
25
+ <span class='fraction'>6/29</span>
26
+ </div>
27
+ <div class='fl pad1y space-right2'>
28
+ <span class="strong">10% </span>
29
+ <span class="quiet">Branches</span>
30
+ <span class='fraction'>1/10</span>
31
+ </div>
32
+ <div class='fl pad1y space-right2'>
33
+ <span class="strong">16.67% </span>
34
+ <span class="quiet">Functions</span>
35
+ <span class='fraction'>1/6</span>
36
+ </div>
37
+ <div class='fl pad1y space-right2'>
38
+ <span class="strong">20.69% </span>
39
+ <span class="quiet">Lines</span>
40
+ <span class='fraction'>6/29</span>
41
+ </div>
42
+ </div>
43
+ <p class="quiet">
44
+ Press <em>n</em> or <em>j</em> to go to the next uncovered block, <em>b</em>, <em>p</em> or <em>k</em> for the previous block.
45
+ </p>
46
+ </div>
47
+ <div class='status-line low'></div>
48
+ <pre><table class="coverage">
49
+ <tr><td class="line-count quiet"><a name='L1'></a><a href='#L1'>1</a>
50
+ <a name='L2'></a><a href='#L2'>2</a>
51
+ <a name='L3'></a><a href='#L3'>3</a>
52
+ <a name='L4'></a><a href='#L4'>4</a>
53
+ <a name='L5'></a><a href='#L5'>5</a>
54
+ <a name='L6'></a><a href='#L6'>6</a>
55
+ <a name='L7'></a><a href='#L7'>7</a>
56
+ <a name='L8'></a><a href='#L8'>8</a>
57
+ <a name='L9'></a><a href='#L9'>9</a>
58
+ <a name='L10'></a><a href='#L10'>10</a>
59
+ <a name='L11'></a><a href='#L11'>11</a>
60
+ <a name='L12'></a><a href='#L12'>12</a>
61
+ <a name='L13'></a><a href='#L13'>13</a>
62
+ <a name='L14'></a><a href='#L14'>14</a>
63
+ <a name='L15'></a><a href='#L15'>15</a>
64
+ <a name='L16'></a><a href='#L16'>16</a>
65
+ <a name='L17'></a><a href='#L17'>17</a>
66
+ <a name='L18'></a><a href='#L18'>18</a>
67
+ <a name='L19'></a><a href='#L19'>19</a>
68
+ <a name='L20'></a><a href='#L20'>20</a>
69
+ <a name='L21'></a><a href='#L21'>21</a>
70
+ <a name='L22'></a><a href='#L22'>22</a>
71
+ <a name='L23'></a><a href='#L23'>23</a>
72
+ <a name='L24'></a><a href='#L24'>24</a>
73
+ <a name='L25'></a><a href='#L25'>25</a>
74
+ <a name='L26'></a><a href='#L26'>26</a>
75
+ <a name='L27'></a><a href='#L27'>27</a>
76
+ <a name='L28'></a><a href='#L28'>28</a>
77
+ <a name='L29'></a><a href='#L29'>29</a>
78
+ <a name='L30'></a><a href='#L30'>30</a>
79
+ <a name='L31'></a><a href='#L31'>31</a>
80
+ <a name='L32'></a><a href='#L32'>32</a>
81
+ <a name='L33'></a><a href='#L33'>33</a>
82
+ <a name='L34'></a><a href='#L34'>34</a>
83
+ <a name='L35'></a><a href='#L35'>35</a>
84
+ <a name='L36'></a><a href='#L36'>36</a>
85
+ <a name='L37'></a><a href='#L37'>37</a>
86
+ <a name='L38'></a><a href='#L38'>38</a>
87
+ <a name='L39'></a><a href='#L39'>39</a>
88
+ <a name='L40'></a><a href='#L40'>40</a>
89
+ <a name='L41'></a><a href='#L41'>41</a>
90
+ <a name='L42'></a><a href='#L42'>42</a>
91
+ <a name='L43'></a><a href='#L43'>43</a>
92
+ <a name='L44'></a><a href='#L44'>44</a>
93
+ <a name='L45'></a><a href='#L45'>45</a>
94
+ <a name='L46'></a><a href='#L46'>46</a>
95
+ <a name='L47'></a><a href='#L47'>47</a>
96
+ <a name='L48'></a><a href='#L48'>48</a>
97
+ <a name='L49'></a><a href='#L49'>49</a>
98
+ <a name='L50'></a><a href='#L50'>50</a>
99
+ <a name='L51'></a><a href='#L51'>51</a>
100
+ <a name='L52'></a><a href='#L52'>52</a>
101
+ <a name='L53'></a><a href='#L53'>53</a>
102
+ <a name='L54'></a><a href='#L54'>54</a>
103
+ <a name='L55'></a><a href='#L55'>55</a>
104
+ <a name='L56'></a><a href='#L56'>56</a>
105
+ <a name='L57'></a><a href='#L57'>57</a></td><td class="line-coverage quiet"><span class="cline-any cline-yes">1x</span>
106
+ <span class="cline-any cline-neutral">&nbsp;</span>
107
+ <span class="cline-any cline-yes">1x</span>
108
+ <span class="cline-any cline-yes">1x</span>
109
+ <span class="cline-any cline-neutral">&nbsp;</span>
110
+ <span class="cline-any cline-yes">1x</span>
111
+ <span class="cline-any cline-yes">2x</span>
112
+ <span class="cline-any cline-no">&nbsp;</span>
113
+ <span class="cline-any cline-no">&nbsp;</span>
114
+ <span class="cline-any cline-no">&nbsp;</span>
115
+ <span class="cline-any cline-neutral">&nbsp;</span>
116
+ <span class="cline-any cline-no">&nbsp;</span>
117
+ <span class="cline-any cline-no">&nbsp;</span>
118
+ <span class="cline-any cline-neutral">&nbsp;</span>
119
+ <span class="cline-any cline-no">&nbsp;</span>
120
+ <span class="cline-any cline-no">&nbsp;</span>
121
+ <span class="cline-any cline-no">&nbsp;</span>
122
+ <span class="cline-any cline-neutral">&nbsp;</span>
123
+ <span class="cline-any cline-neutral">&nbsp;</span>
124
+ <span class="cline-any cline-neutral">&nbsp;</span>
125
+ <span class="cline-any cline-no">&nbsp;</span>
126
+ <span class="cline-any cline-no">&nbsp;</span>
127
+ <span class="cline-any cline-neutral">&nbsp;</span>
128
+ <span class="cline-any cline-no">&nbsp;</span>
129
+ <span class="cline-any cline-neutral">&nbsp;</span>
130
+ <span class="cline-any cline-neutral">&nbsp;</span>
131
+ <span class="cline-any cline-no">&nbsp;</span>
132
+ <span class="cline-any cline-no">&nbsp;</span>
133
+ <span class="cline-any cline-neutral">&nbsp;</span>
134
+ <span class="cline-any cline-neutral">&nbsp;</span>
135
+ <span class="cline-any cline-no">&nbsp;</span>
136
+ <span class="cline-any cline-no">&nbsp;</span>
137
+ <span class="cline-any cline-no">&nbsp;</span>
138
+ <span class="cline-any cline-neutral">&nbsp;</span>
139
+ <span class="cline-any cline-no">&nbsp;</span>
140
+ <span class="cline-any cline-no">&nbsp;</span>
141
+ <span class="cline-any cline-no">&nbsp;</span>
142
+ <span class="cline-any cline-neutral">&nbsp;</span>
143
+ <span class="cline-any cline-neutral">&nbsp;</span>
144
+ <span class="cline-any cline-neutral">&nbsp;</span>
145
+ <span class="cline-any cline-neutral">&nbsp;</span>
146
+ <span class="cline-any cline-neutral">&nbsp;</span>
147
+ <span class="cline-any cline-no">&nbsp;</span>
148
+ <span class="cline-any cline-no">&nbsp;</span>
149
+ <span class="cline-any cline-neutral">&nbsp;</span>
150
+ <span class="cline-any cline-neutral">&nbsp;</span>
151
+ <span class="cline-any cline-no">&nbsp;</span>
152
+ <span class="cline-any cline-no">&nbsp;</span>
153
+ <span class="cline-any cline-neutral">&nbsp;</span>
154
+ <span class="cline-any cline-neutral">&nbsp;</span>
155
+ <span class="cline-any cline-neutral">&nbsp;</span>
156
+ <span class="cline-any cline-yes">2x</span>
157
+ <span class="cline-any cline-neutral">&nbsp;</span>
158
+ <span class="cline-any cline-neutral">&nbsp;</span>
159
+ <span class="cline-any cline-neutral">&nbsp;</span>
160
+ <span class="cline-any cline-neutral">&nbsp;</span>
161
+ <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var helpers = require(__dirname + "/helpers");
162
+ &nbsp;
163
+ var sifToGrnsight = require(__dirname + "/importers/sif");
164
+ var graphMlToGrnsight = require(__dirname + "/importers/graphml");
165
+ &nbsp;
166
+ module.exports = function (app) {
167
+ <span class="missing-if-branch" title="if path not taken" >I</span>if (app) {
168
+ var multiparty = <span class="cstat-no" title="statement not covered" >require("multiparty");</span>
169
+ var path = <span class="cstat-no" title="statement not covered" >require("path");</span>
170
+ var fs = <span class="cstat-no" title="statement not covered" >require("fs");</span>
171
+ &nbsp;
172
+ var <span class="fstat-no" title="function not covered" >performUpload = <span class="cstat-no" title="statement not covered" >f</span>unction (req, res, extension, importer) {</span>
173
+ <span class="cstat-no" title="statement not covered" > helpers.attachCorsHeader(res, app);</span>
174
+ &nbsp;
175
+ (<span class="cstat-no" title="statement not covered" >new multiparty.Form()).parse(req, <span class="fstat-no" title="function not covered" >function (</span>error, fields, files) {</span>
176
+ <span class="cstat-no" title="statement not covered" > if (error) {</span>
177
+ <span class="cstat-no" title="statement not covered" > return res.send(400, "There was a problem uploading your file. Please try again.");</span>
178
+ }
179
+ &nbsp;
180
+ var input;
181
+ <span class="cstat-no" title="statement not covered" > try {</span>
182
+ <span class="cstat-no" title="statement not covered" > input = files.file[0].path;</span>
183
+ } catch (error) {
184
+ <span class="cstat-no" title="statement not covered" > return res.send(400, "No import file selected.");</span>
185
+ }
186
+ &nbsp;
187
+ <span class="cstat-no" title="statement not covered" > if (path.extname(input) !== "." + extension) {</span>
188
+ <span class="cstat-no" title="statement not covered" > return res.send(400, "The filename does not end in ." + extension + ".");</span>
189
+ }
190
+ &nbsp;
191
+ <span class="cstat-no" title="statement not covered" > fs.readFile(input, { encoding: "utf-8" }, <span class="fstat-no" title="function not covered" >function (</span>error, data) {</span>
192
+ <span class="cstat-no" title="statement not covered" > if (error) {</span>
193
+ <span class="cstat-no" title="statement not covered" > throw error;</span>
194
+ } else {
195
+ <span class="cstat-no" title="statement not covered" > helpers.attachFileHeaders(res, input);</span>
196
+ var network = <span class="cstat-no" title="statement not covered" >importer(data);</span>
197
+ <span class="cstat-no" title="statement not covered" > return res.status((network.errors.length === 0) ? 200 : 400).json(network);</span>
198
+ }
199
+ });
200
+ });
201
+ };
202
+ &nbsp;
203
+ <span class="cstat-no" title="statement not covered" > app.post("/upload-sif", <span class="fstat-no" title="function not covered" >function (</span>req, res) {</span>
204
+ <span class="cstat-no" title="statement not covered" > performUpload(req, res, "sif", sifToGrnsight);</span>
205
+ });
206
+ &nbsp;
207
+ <span class="cstat-no" title="statement not covered" > app.post("/upload-graphml", <span class="fstat-no" title="function not covered" >function (</span>req, res) {</span>
208
+ <span class="cstat-no" title="statement not covered" > performUpload(req, res, "graphml", graphMlToGrnsight);</span>
209
+ });
210
+ }
211
+ &nbsp;
212
+ return {
213
+ sifToGrnsight: sifToGrnsight,
214
+ graphMlToGrnsight: graphMlToGrnsight
215
+ };
216
+ };
217
+ &nbsp;</pre></td></tr>
218
+ </table></pre>
219
+ <div class='push'></div><!-- for sticky footer -->
220
+ </div><!-- /wrapper -->
221
+ <div class='footer quiet pad2 space-top1 center small'>
222
+ Code coverage
223
+ generated by <a href="https://istanbul.js.org/" target="_blank">istanbul</a> at Thu May 31 2018 15:29:57 GMT-0700 (PDT)
224
+ </div>
225
+ </div>
226
+ <script src="../../prettify.js"></script>
227
+ <script>
228
+ window.onload = function () {
229
+ if (typeof prettyPrint === 'function') {
230
+ prettyPrint();
231
+ }
232
+ };
233
+ </script>
234
+ <script src="../../sorter.js"></script>
235
+ <script src="../../block-navigation.js"></script>
236
+ </body>
237
+ </html>