gfdnavi 1.3.0.0

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 (446) hide show
  1. data/ChangeLog +10949 -0
  2. data/LICENCE.txt +57 -0
  3. data/Makefile +18 -0
  4. data/TODO +132 -0
  5. data/app/controllers/analysis_controller.rb +700 -0
  6. data/app/controllers/application.rb +41 -0
  7. data/app/controllers/draw_method_controller.rb +172 -0
  8. data/app/controllers/explorer_controller.rb +197 -0
  9. data/app/controllers/finder_controller.rb +331 -0
  10. data/app/controllers/function_controller.rb +204 -0
  11. data/app/controllers/group_controller.rb +115 -0
  12. data/app/controllers/keyword_attributes_controller.rb +52 -0
  13. data/app/controllers/knowledge_controller.rb +928 -0
  14. data/app/controllers/nodes_controller.rb +515 -0
  15. data/app/controllers/search_controller.rb +341 -0
  16. data/app/controllers/user_controller.rb +337 -0
  17. data/app/helpers/analysis_helper.rb +2 -0
  18. data/app/helpers/application_helper.rb +105 -0
  19. data/app/helpers/description_helper.rb +2 -0
  20. data/app/helpers/function_helper.rb +2 -0
  21. data/app/helpers/group_helper.rb +2 -0
  22. data/app/helpers/search_helper.rb +3 -0
  23. data/app/helpers/user_helper.rb +2 -0
  24. data/app/helpers/work_flow_helper.rb +92 -0
  25. data/app/models/actual_file.rb +3 -0
  26. data/app/models/analysis.rb +715 -0
  27. data/app/models/analysis_history.rb +42 -0
  28. data/app/models/cross_array.rb +22 -0
  29. data/app/models/cross_result.rb +254 -0
  30. data/app/models/derived_spatial_attribute.rb +3 -0
  31. data/app/models/diagram_cache.rb +16 -0
  32. data/app/models/diagram_cache_datum.rb +4 -0
  33. data/app/models/diagram_cache_session.rb +8 -0
  34. data/app/models/directory.rb +21 -0
  35. data/app/models/draw_method.rb +48 -0
  36. data/app/models/draw_method_attribute.rb +8 -0
  37. data/app/models/draw_parameter.rb +12 -0
  38. data/app/models/explorer_query.rb +354 -0
  39. data/app/models/explorer_result.rb +312 -0
  40. data/app/models/function.rb +75 -0
  41. data/app/models/function_argument.rb +6 -0
  42. data/app/models/function_output.rb +4 -0
  43. data/app/models/group.rb +153 -0
  44. data/app/models/image.rb +20 -0
  45. data/app/models/keyword_attribute.rb +179 -0
  46. data/app/models/knowledge.rb +94 -0
  47. data/app/models/knowledge_backup.rb +32 -0
  48. data/app/models/knowledge_figure.rb +16 -0
  49. data/app/models/knowledge_figure_backup.rb +16 -0
  50. data/app/models/knowledge_parser.rb +392 -0
  51. data/app/models/node.rb +605 -0
  52. data/app/models/node_entity_abstract.rb +112 -0
  53. data/app/models/node_lineage.rb +6 -0
  54. data/app/models/node_relation.rb +4 -0
  55. data/app/models/path_node.rb +60 -0
  56. data/app/models/query.rb +193 -0
  57. data/app/models/query_history.rb +12 -0
  58. data/app/models/results.rb +48 -0
  59. data/app/models/sign_up_user.rb +25 -0
  60. data/app/models/spatial_and_time_attribute.rb +11 -0
  61. data/app/models/user.rb +115 -0
  62. data/app/models/user_mailer.rb +48 -0
  63. data/app/models/value_type.rb +3 -0
  64. data/app/models/variable.rb +70 -0
  65. data/app/models/virtual_node.rb +457 -0
  66. data/app/views/analysis/__help_analysis_tab.en.html +57 -0
  67. data/app/views/analysis/__help_draw_share.en.html +12 -0
  68. data/app/views/analysis/__help_draw_tab.en.html +6 -0
  69. data/app/views/analysis/_analysis_function_settings.rhtml +61 -0
  70. data/app/views/analysis/_analysis_settings.rhtml +28 -0
  71. data/app/views/analysis/_diagram.rhtml +70 -0
  72. data/app/views/analysis/_dimension_option.rhtml +59 -0
  73. data/app/views/analysis/_draw_general_settings.rhtml +217 -0
  74. data/app/views/analysis/_draw_settings.rhtml +73 -0
  75. data/app/views/analysis/_history.rhtml +19 -0
  76. data/app/views/analysis/_popular_diagrams.rhtml +42 -0
  77. data/app/views/analysis/_save_form.rhtml +44 -0
  78. data/app/views/analysis/_variables.rhtml +66 -0
  79. data/app/views/analysis/_variables_order.rhtml +56 -0
  80. data/app/views/analysis/index.rhtml +195 -0
  81. data/app/views/analysis/preview.rhtml +3 -0
  82. data/app/views/analysis/save.rhtml +73 -0
  83. data/app/views/analysis/show_diagram.rhtml +42 -0
  84. data/app/views/cross/_display_map.rhtml +201 -0
  85. data/app/views/cross/_result.rhtml +205 -0
  86. data/app/views/cross/_show_result_tree.rhtml +40 -0
  87. data/app/views/cross/_show_results.rhtml +80 -0
  88. data/app/views/cross/_style.rhtml +21 -0
  89. data/app/views/cross/index.rhtml +271 -0
  90. data/app/views/draw_method/_edit_form.rhtml +110 -0
  91. data/app/views/draw_method/create.rhtml +8 -0
  92. data/app/views/draw_method/details.rhtml +113 -0
  93. data/app/views/draw_method/edit.rhtml +8 -0
  94. data/app/views/draw_method/list.rhtml +80 -0
  95. data/app/views/explorer/_display_map.rhtml +199 -0
  96. data/app/views/explorer/_show_result_tree.rhtml +40 -0
  97. data/app/views/explorer/_show_results.rhtml +101 -0
  98. data/app/views/explorer/_style.rhtml +21 -0
  99. data/app/views/explorer/index.rhtml +214 -0
  100. data/app/views/finder/_children.html.erb +84 -0
  101. data/app/views/finder/_children_details.html.erb +74 -0
  102. data/app/views/finder/_children_details_tr.html.erb +196 -0
  103. data/app/views/finder/create_tree.html.erb +15 -0
  104. data/app/views/finder/flex.html.erb +52 -0
  105. data/app/views/finder/index.html.erb +47 -0
  106. data/app/views/finder/show_details.html.erb +3 -0
  107. data/app/views/finder/show_images.html.erb +3 -0
  108. data/app/views/function/_edit_form.rhtml +106 -0
  109. data/app/views/function/create.rhtml +8 -0
  110. data/app/views/function/details.rhtml +96 -0
  111. data/app/views/function/edit.rhtml +8 -0
  112. data/app/views/function/list.rhtml +80 -0
  113. data/app/views/group/add_member.rhtml +13 -0
  114. data/app/views/group/change_owner.rhtml +15 -0
  115. data/app/views/group/create.rhtml +11 -0
  116. data/app/views/group/delete_member.rhtml +14 -0
  117. data/app/views/group/list.rhtml +63 -0
  118. data/app/views/knowledge/_backup.rhtml +135 -0
  119. data/app/views/knowledge/_category.rhtml +58 -0
  120. data/app/views/knowledge/_category_list.rhtml +34 -0
  121. data/app/views/knowledge/_category_table.rhtml +23 -0
  122. data/app/views/knowledge/_comment.rhtml +64 -0
  123. data/app/views/knowledge/_comment_input_form.rhtml +19 -0
  124. data/app/views/knowledge/_comments.rhtml +84 -0
  125. data/app/views/knowledge/_form.rhtml +139 -0
  126. data/app/views/knowledge/_group_figure_form.rhtml +187 -0
  127. data/app/views/knowledge/_layout_figure.rhtml +61 -0
  128. data/app/views/knowledge/_layout_figures_in_a_row_above_text.rhtml +42 -0
  129. data/app/views/knowledge/_layout_figures_under_text.rhtml +45 -0
  130. data/app/views/knowledge/_layout_one_figure_above_text.rhtml +28 -0
  131. data/app/views/knowledge/_summary.rhtml +21 -0
  132. data/app/views/knowledge/edit.rhtml +37 -0
  133. data/app/views/knowledge/list.rhtml +287 -0
  134. data/app/views/knowledge/new.rhtml +23 -0
  135. data/app/views/knowledge/new_from_analysis.rhtml +21 -0
  136. data/app/views/knowledge/show.rhtml +196 -0
  137. data/app/views/layouts/gfdnavi.rhtml +105 -0
  138. data/app/views/nodes/_ancestors.html.erb +89 -0
  139. data/app/views/nodes/_description_methods_table.html.erb +75 -0
  140. data/app/views/nodes/_mode.html.erb +16 -0
  141. data/app/views/nodes/description.html.erb +181 -0
  142. data/app/views/nodes/description_methods.html.erb +1 -0
  143. data/app/views/nodes/edit.html.erb +73 -0
  144. data/app/views/nodes/index.html.erb +25 -0
  145. data/app/views/nodes/show.html.erb +20 -0
  146. data/app/views/search/_children_details_mapsearch.rhtml +68 -0
  147. data/app/views/search/_children_details_tr.rhtml +205 -0
  148. data/app/views/search/_show_grouplist.rhtml +74 -0
  149. data/app/views/search/_show_results.rhtml +43 -0
  150. data/app/views/search/_show_results_global.rhtml +36 -0
  151. data/app/views/search/_show_results_partial.rhtml +39 -0
  152. data/app/views/search/_show_results_partial_groupbyfile.rhtml +50 -0
  153. data/app/views/search/_show_variablelist.rhtml +28 -0
  154. data/app/views/search/mapsearch.rhtml +176 -0
  155. data/app/views/search/remapsearch.rjs +18 -0
  156. data/app/views/search/show_details.rhtml +3 -0
  157. data/app/views/user/add_user.rhtml +30 -0
  158. data/app/views/user/change_password.rhtml +25 -0
  159. data/app/views/user/edit.html.erb +50 -0
  160. data/app/views/user/index.rhtml +162 -0
  161. data/app/views/user/login.rhtml +41 -0
  162. data/app/views/user/logout.rhtml +4 -0
  163. data/app/views/user/signup.rhtml +36 -0
  164. data/app/views/user/signup_succeeded.rhtml +36 -0
  165. data/app/views/user_mailer/authorization_inform.rhtml +15 -0
  166. data/app/views/user_mailer/signup_accepted.rhtml +12 -0
  167. data/app/views/user_mailer/signup_confirm.rhtml +14 -0
  168. data/app/views/user_mailer/signup_inform.rhtml +13 -0
  169. data/app/views/user_mailer/signup_rejected.rhtml +11 -0
  170. data/app/views/work_flow/_push_wsdls.rhtml +55 -0
  171. data/app/views/work_flow/index.rhtml +46 -0
  172. data/config/database.yml.example +35 -0
  173. data/config/environment.rb +68 -0
  174. data/config/gfdnavi.yml.example +95 -0
  175. data/config/load_config.rb +151 -0
  176. data/config/routes.rb +35 -0
  177. data/consistency_checker.rb +129 -0
  178. data/data/gfdnavi_docs/how_to_draw_multiple_images.knlge +68 -0
  179. data/data/gfdnavi_docs/how_to_knowledge.knlge +138 -0
  180. data/data/gfdnavi_docs/how_to_write_document_about_Gfdnavi.knlge +30 -0
  181. data/data/samples/jmadata.SIGEN +8 -0
  182. data/data/samples/jmadata.yml +6 -0
  183. data/data/samples/jmadata/MSM-P/2006.nc.yml +2 -0
  184. data/data/samples/jmadata/MSM-P/2006.yml +17 -0
  185. data/data/samples/jmadata/MSM-P/2006/0101.nc +0 -0
  186. data/data/samples/jmadata/MSM-P/2006/0101.nc.yml +13 -0
  187. data/data/samples/jmadata/MSM-P/2006/0102.nc +0 -0
  188. data/data/samples/jmadata/MSM-P/2006/0103.nc +0 -0
  189. data/data/samples/jmadata/MSM-P/2006/0104.nc +0 -0
  190. data/data/samples/jmadata/MSM-P/2006/0105.nc +0 -0
  191. data/data/samples/jmadata/MSM-P/2006/010[1-3].nc.yml +2 -0
  192. data/data/samples/jmadata/MSM-P/2006/skip_data.rb +96 -0
  193. data/data/samples/jmadata/MSM-P/2006/skip_data.sh +6 -0
  194. data/data/samples/reanalysis.SIGEN +8 -0
  195. data/data/samples/reanalysis/era40.SIGEN +8 -0
  196. data/data/samples/reanalysis/era40.yml +2 -0
  197. data/data/samples/reanalysis/era40/t.jan.nc +0 -0
  198. data/data/samples/reanalysis/era40/t.jan.nc.yml +1 -0
  199. data/data/samples/reanalysis/ncep.SIGEN +9 -0
  200. data/data/samples/reanalysis/ncep/T.jan.100hPa.png +0 -0
  201. data/data/samples/reanalysis/ncep/T.jan.100hPa.png.yml +43 -0
  202. data/data/samples/reanalysis/ncep/T.jan.nc +0 -0
  203. data/data/samples/reanalysis/ncep/T.jan.zonal_mean.nc +0 -0
  204. data/data/samples/reanalysis/ncep/T.jan.zonal_mean.nc.yml +8 -0
  205. data/data/samples/reanalysis/ncep/T.jan_only_root.nc +0 -0
  206. data/data/samples/reanalysis/ncep/T.jan_only_root.nc.yml +4 -0
  207. data/data/samples/reanalysis/ncep/UV.jan.nc +0 -0
  208. data/data/samples/reanalysis/ncep/UV.jan.nc.yml +10 -0
  209. data/data/samples/reanalysis/ncep/UV.jan.nc.yml.ja +11 -0
  210. data/data/samples/sonde_operational.yml +5 -0
  211. data/data/samples/sonde_operational/std_plev.yml +12 -0
  212. data/data/samples/sonde_operational/std_plev/41256.spl.nc +0 -0
  213. data/data/samples/sonde_operational/std_plev/42410.spl.nc +0 -0
  214. data/data/samples/sonde_operational/std_plev/43333.spl.nc +0 -0
  215. data/data/samples/sonde_operational/std_plev/43346.spl.nc +0 -0
  216. data/data/samples/sonde_operational/std_plev/48698.spl.nc +0 -0
  217. data/data/samples/sonde_operational/std_plev/61641.spl.nc +0 -0
  218. data/data/samples/sonde_operational/std_plev/63741.spl.nc +0 -0
  219. data/data/samples/sonde_operational/std_plev/67083.spl.nc +0 -0
  220. data/data/samples/sonde_operational/std_plev/72261.spl.nc +0 -0
  221. data/data/samples/sonde_operational/std_plev/76805.spl.nc +0 -0
  222. data/data/samples/sonde_operational/std_plev/82193.spl.nc +0 -0
  223. data/data/samples/sonde_operational/std_plev/91165.spl.nc +0 -0
  224. data/data/samples/sonde_operational/std_plev/91610.spl.nc +0 -0
  225. data/data/samples/sonde_operational/std_plev/91948.spl.nc +0 -0
  226. data/data/samples/sonde_operational/std_plev/94294.spl.nc +0 -0
  227. data/db/NetCDFparser.rb +406 -0
  228. data/db/create_derived_spatial_attributes.sql +12 -0
  229. data/db/draw_methods/line.yml +6 -0
  230. data/db/draw_methods/scatter.yml +38 -0
  231. data/db/draw_methods/tone.yml +64 -0
  232. data/db/draw_methods/vector.yml +19 -0
  233. data/db/dump_db.rb +43 -0
  234. data/db/functions/additions.yml +10 -0
  235. data/db/functions/cut.yml +10 -0
  236. data/db/functions/division.yml +10 -0
  237. data/db/functions/mean.yml +28 -0
  238. data/db/functions/multiplication.yml +10 -0
  239. data/db/functions/stddev.yml +28 -0
  240. data/db/functions/subtraction.yml +10 -0
  241. data/db/migrate/001_initial_scheme.rb +289 -0
  242. data/db/migrate/002_add_open_id_authentication_tables.rb +20 -0
  243. data/db/register_directory_tree.rb +760 -0
  244. data/db/restore_db.rb +60 -0
  245. data/gfdnavi-install +828 -0
  246. data/install.rb +828 -0
  247. data/lib/activerecord_gfdnavi.rb +31 -0
  248. data/lib/basic_authorization.rb +50 -0
  249. data/lib/create_activeresources.rb +108 -0
  250. data/lib/execute_analysis.rb +472 -0
  251. data/lib/file_gfdnavi.rb +38 -0
  252. data/lib/gphys_gfdnavi.rb +81 -0
  253. data/lib/localdir.rb +110 -0
  254. data/lib/login_system.rb +110 -0
  255. data/lib/multibytes.rb +20 -0
  256. data/lib/narray_yaml.rb +58 -0
  257. data/lib/no_rdb_base.rb +40 -0
  258. data/lib/opendapdir.rb +171 -0
  259. data/lib/tar.rb +127 -0
  260. data/lib/tasks/clean.rake +65 -0
  261. data/lib/tasks/setup.rake +316 -0
  262. data/lib/tasks/update.rake +62 -0
  263. data/lib/vizshot_gfdnavi.rb +224 -0
  264. data/public/crossdomain.xml +4 -0
  265. data/public/flex/NodeTreeDescriptor.as +55 -0
  266. data/public/flex/TreeNode.as +253 -0
  267. data/public/flex/finder.mxml +304 -0
  268. data/public/flex/finder.swf +0 -0
  269. data/public/flex/gfdnavi.mxml +52 -0
  270. data/public/flex/gfdnavi.swf +0 -0
  271. data/public/images/Help_S-shots/dir_tree_with_add.jpg +0 -0
  272. data/public/images/analyze.gif +0 -0
  273. data/public/images/circle.gif +0 -0
  274. data/public/images/create_from_analysis_button.png +0 -0
  275. data/public/images/delete.png +0 -0
  276. data/public/images/down.png +0 -0
  277. data/public/images/drawbutton.gif +0 -0
  278. data/public/images/gfdnavi_home_logo.png +0 -0
  279. data/public/images/gfdnavi_logo_big.png +0 -0
  280. data/public/images/gfdnavi_logo_med.png +0 -0
  281. data/public/images/gfdnavi_logo_mini.png +0 -0
  282. data/public/images/gfdnavi_logo_nobg_big.png +0 -0
  283. data/public/images/gfdnavi_logo_nobg_med.png +0 -0
  284. data/public/images/gfdnavi_logo_nobg_small.png +0 -0
  285. data/public/images/gfdnavi_logo_small.png +0 -0
  286. data/public/images/gfdnavi_logo_xsmall.png +0 -0
  287. data/public/images/hbar.png +0 -0
  288. data/public/images/helpmark16.png +0 -0
  289. data/public/images/helpmark18.png +0 -0
  290. data/public/images/kikyu_g.gif +0 -0
  291. data/public/images/kikyu_r.gif +0 -0
  292. data/public/images/map_icon_g.gif +0 -0
  293. data/public/images/map_icon_r.gif +0 -0
  294. data/public/images/new_knowledge.png +0 -0
  295. data/public/images/openid.png +0 -0
  296. data/public/images/read_in_the_form.png +0 -0
  297. data/public/images/slider_f.gif +0 -0
  298. data/public/images/slider_f_red.gif +0 -0
  299. data/public/images/star1.gif +0 -0
  300. data/public/images/star2.gif +0 -0
  301. data/public/images/startanim.gif +0 -0
  302. data/public/images/stopanim.gif +0 -0
  303. data/public/images/tree/DL.png +0 -0
  304. data/public/images/tree/anal_viz.png +0 -0
  305. data/public/images/tree/analyze_visualize_checked_items.png +0 -0
  306. data/public/images/tree/binary.png +0 -0
  307. data/public/images/tree/details.png +0 -0
  308. data/public/images/tree/download_checked_items.png +0 -0
  309. data/public/images/tree/folder.png +0 -0
  310. data/public/images/tree/folder_close.gif +0 -0
  311. data/public/images/tree/image2.png +0 -0
  312. data/public/images/tree/knowledge.png +0 -0
  313. data/public/images/tree/knowledges.png +0 -0
  314. data/public/images/tree/last.gif +0 -0
  315. data/public/images/tree/last.png +0 -0
  316. data/public/images/tree/minus.gif +0 -0
  317. data/public/images/tree/minus_simple.gif +0 -0
  318. data/public/images/tree/none.gif +0 -0
  319. data/public/images/tree/none.png +0 -0
  320. data/public/images/tree/plus.gif +0 -0
  321. data/public/images/tree/plus_simple.gif +0 -0
  322. data/public/images/tree/show.png +0 -0
  323. data/public/images/tree/show_checked_items.png +0 -0
  324. data/public/images/tree/t.gif +0 -0
  325. data/public/images/tree/t.png +0 -0
  326. data/public/images/tree/tate.gif +0 -0
  327. data/public/images/tree/tate.png +0 -0
  328. data/public/images/up.png +0 -0
  329. data/public/images/vbar.png +0 -0
  330. data/public/images/white.bmp +0 -0
  331. data/public/images/x.gif +0 -0
  332. data/public/index.html +100 -0
  333. data/public/javascripts/AC_OETags.js +269 -0
  334. data/public/javascripts/analysis.js +751 -0
  335. data/public/javascripts/application.js +29 -0
  336. data/public/javascripts/directory_tree.js +102 -0
  337. data/public/javascripts/draw_method.js +83 -0
  338. data/public/javascripts/excanvas.js +704 -0
  339. data/public/javascripts/function.js +107 -0
  340. data/public/javascripts/gfdnavi.js +175 -0
  341. data/public/javascripts/knowledge.js +384 -0
  342. data/public/javascripts/mapsearch.js +313 -0
  343. data/public/javascripts/progress.js +42 -0
  344. data/public/javascripts/resizable_box.js +164 -0
  345. data/public/javascripts/slider.js +260 -0
  346. data/public/javascripts/tab.js +17 -0
  347. data/public/javascripts/work_flow.js +452 -0
  348. data/public/stylesheets/analysis.css +111 -0
  349. data/public/stylesheets/description.css +71 -0
  350. data/public/stylesheets/gfdnavi.css +141 -0
  351. data/public/stylesheets/knowledge.css +218 -0
  352. data/public/stylesheets/search.css +184 -0
  353. data/public/stylesheets/tree.css +45 -0
  354. data/public/stylesheets/tree_for_ie.css +3 -0
  355. data/public/stylesheets/work_flow.css +78 -0
  356. data/script/cleaner +11 -0
  357. data/script/server_ssl +131 -0
  358. data/test/fixtures/diagram_cache_data.yml +5 -0
  359. data/test/fixtures/diagram_cache_sessions.yml +6 -0
  360. data/test/fixtures/diagram_caches.yml +6 -0
  361. data/test/fixtures/directories.yml +57 -0
  362. data/test/fixtures/draw_parameters.yml +6 -0
  363. data/test/fixtures/function_arguments.yml +15 -0
  364. data/test/fixtures/function_outputs.yml +15 -0
  365. data/test/fixtures/functions.yml +29 -0
  366. data/test/fixtures/group_members.yml +33 -0
  367. data/test/fixtures/groups.yml +25 -0
  368. data/test/fixtures/images.yml +12 -0
  369. data/test/fixtures/keyword_attributes.yml +73 -0
  370. data/test/fixtures/knowledges.yml +10 -0
  371. data/test/fixtures/node_relations.yml +11 -0
  372. data/test/fixtures/nodes.yml +298 -0
  373. data/test/fixtures/sign_up_users.yml +8 -0
  374. data/test/fixtures/spatial_and_time_attributes.yml +29 -0
  375. data/test/fixtures/user_mailer/authorization_inform +11 -0
  376. data/test/fixtures/user_mailer/signup_accepted +10 -0
  377. data/test/fixtures/user_mailer/signup_confirm +17 -0
  378. data/test/fixtures/user_mailer/signup_inform +10 -0
  379. data/test/fixtures/user_mailer/signup_rejected +9 -0
  380. data/test/fixtures/users.yml +31 -0
  381. data/test/fixtures/value_types.yml +10 -0
  382. data/test/fixtures/variables.yml +17 -0
  383. data/test/functional/analysis_controller_test.rb +169 -0
  384. data/test/functional/description_controller_test.rb +18 -0
  385. data/test/functional/function_controller_test.rb +18 -0
  386. data/test/functional/group_controller_test.rb +18 -0
  387. data/test/functional/search_controller_test.rb +83 -0
  388. data/test/functional/user_controller_test.rb +77 -0
  389. data/test/functional/webservice_analysis_api_test.rb +12 -0
  390. data/test/functional/work_flow_controller_test.rb +18 -0
  391. data/test/test_helper.rb +28 -0
  392. data/test/unit/diagram_cache_datum_test.rb +10 -0
  393. data/test/unit/diagram_cache_session_test.rb +10 -0
  394. data/test/unit/diagram_cache_test.rb +10 -0
  395. data/test/unit/directory_test.rb +49 -0
  396. data/test/unit/draw_parameter_test.rb +10 -0
  397. data/test/unit/function_argument_test.rb +10 -0
  398. data/test/unit/function_output_test.rb +10 -0
  399. data/test/unit/function_test.rb +10 -0
  400. data/test/unit/group_test.rb +48 -0
  401. data/test/unit/image_test.rb +13 -0
  402. data/test/unit/keyword_attribute_test.rb +33 -0
  403. data/test/unit/knowledge_test.rb +13 -0
  404. data/test/unit/node_relation_test.rb +20 -0
  405. data/test/unit/node_test.rb +85 -0
  406. data/test/unit/sign_up_user_test.rb +20 -0
  407. data/test/unit/spatial_and_time_attribute_test.rb +29 -0
  408. data/test/unit/user_mailer_test.rb +101 -0
  409. data/test/unit/user_test.rb +134 -0
  410. data/test/unit/value_type_test.rb +10 -0
  411. data/test/unit/variable_test.rb +35 -0
  412. data/vendor/plugins/acts_as_list/README +23 -0
  413. data/vendor/plugins/acts_as_list/init.rb +3 -0
  414. data/vendor/plugins/acts_as_list/lib/active_record/acts/list.rb +256 -0
  415. data/vendor/plugins/acts_as_list/test/list_test.rb +332 -0
  416. data/vendor/plugins/acts_as_tree/README +26 -0
  417. data/vendor/plugins/acts_as_tree/Rakefile +22 -0
  418. data/vendor/plugins/acts_as_tree/init.rb +1 -0
  419. data/vendor/plugins/acts_as_tree/lib/active_record/acts/tree.rb +96 -0
  420. data/vendor/plugins/acts_as_tree/test/abstract_unit.rb +0 -0
  421. data/vendor/plugins/acts_as_tree/test/acts_as_tree_test.rb +219 -0
  422. data/vendor/plugins/acts_as_tree/test/database.yml +0 -0
  423. data/vendor/plugins/acts_as_tree/test/fixtures/mixin.rb +0 -0
  424. data/vendor/plugins/acts_as_tree/test/fixtures/mixins.yml +0 -0
  425. data/vendor/plugins/acts_as_tree/test/schema.rb +0 -0
  426. data/vendor/plugins/will_paginate/CHANGELOG +92 -0
  427. data/vendor/plugins/will_paginate/LICENSE +18 -0
  428. data/vendor/plugins/will_paginate/README.rdoc +131 -0
  429. data/vendor/plugins/will_paginate/Rakefile +62 -0
  430. data/vendor/plugins/will_paginate/examples/apple-circle.gif +0 -0
  431. data/vendor/plugins/will_paginate/examples/index.haml +69 -0
  432. data/vendor/plugins/will_paginate/examples/index.html +92 -0
  433. data/vendor/plugins/will_paginate/examples/pagination.css +90 -0
  434. data/vendor/plugins/will_paginate/examples/pagination.sass +91 -0
  435. data/vendor/plugins/will_paginate/init.rb +1 -0
  436. data/vendor/plugins/will_paginate/lib/will_paginate.rb +86 -0
  437. data/vendor/plugins/will_paginate/lib/will_paginate/array.rb +16 -0
  438. data/vendor/plugins/will_paginate/lib/will_paginate/collection.rb +145 -0
  439. data/vendor/plugins/will_paginate/lib/will_paginate/core_ext.rb +32 -0
  440. data/vendor/plugins/will_paginate/lib/will_paginate/finder.rb +247 -0
  441. data/vendor/plugins/will_paginate/lib/will_paginate/named_scope.rb +132 -0
  442. data/vendor/plugins/will_paginate/lib/will_paginate/named_scope_patch.rb +39 -0
  443. data/vendor/plugins/will_paginate/lib/will_paginate/version.rb +9 -0
  444. data/vendor/plugins/will_paginate/lib/will_paginate/view_helpers.rb +373 -0
  445. data/vendor/plugins/will_paginate/will_paginate.gemspec +21 -0
  446. metadata +586 -0
@@ -0,0 +1,32 @@
1
+ class KnowledgeBackup < ActiveRecord::Base
2
+
3
+ has_many :knowledge_figure_backups, :dependent => :destroy
4
+
5
+ # validates_length_of :title, :within => 0..400
6
+ validates_length_of :textbody, :within => 0..100000
7
+
8
+ #<< class methods >>
9
+
10
+ class << self
11
+ def new_comment_number_from_parent_document(parent_knowledge_id, user)
12
+ comments = Knowledge.find(:all, :conditions => ["comment_on = ? AND comment_number IS NOT NULL", parent_knowledge_id], :user => user)
13
+ if comments.length > 0
14
+ comments.collect! {|comment|
15
+ comment = comment.comment_number
16
+ }
17
+ comment_number = comments.max + 1
18
+ else
19
+ comment_number = 1
20
+ end
21
+ end
22
+
23
+ # copy of ./node.rb
24
+ def set_rgroups(*groups)
25
+ groups = groups[0] if groups.length==1 and groups[0].is_a?(Array)
26
+ self.rgroups = Group.bit_mask_for(*groups)
27
+ end
28
+ end
29
+ end
30
+
31
+
32
+
@@ -0,0 +1,16 @@
1
+ class KnowledgeFigure < ActiveRecord::Base
2
+ belongs_to :knowledge
3
+ belongs_to :image, :class_name=>"Image", :foreign_key=>'image_id'
4
+
5
+ validates_length_of :caption, :within => 0..5000
6
+
7
+ alias :__image__ :image
8
+ def image
9
+ image = __image__
10
+ raise("#{path} is a GPhys, not a figure.") if image.gphysizable?
11
+ image
12
+ end
13
+
14
+ end
15
+
16
+
@@ -0,0 +1,16 @@
1
+ class KnowledgeFigureBackup < ActiveRecord::Base
2
+ belongs_to :knowledge_backup
3
+ belongs_to :image, :class_name=>"Image", :foreign_key=>'image_id'
4
+
5
+ validates_length_of :caption, :within => 0..5000
6
+
7
+ alias :__image__ :image
8
+ def image
9
+ image = __image__
10
+ raise("#{path} is a GPhys, not a figure.") if image.gphysizable?
11
+ image
12
+ end
13
+
14
+ end
15
+
16
+
@@ -0,0 +1,392 @@
1
+ # = Gfdnavi��knowledge�h�L�������g�����߂� RD �`���̕��͂��p�[�X����B
2
+ # == ���p��
3
+ # rdp = RDParser.new( rdstring )
4
+ # tree = rdp.make_tree # parse����
5
+ # tree.parse # html�ɕϊ�����
6
+ #
7
+ # == knowledge�h�L�������g�̎d�l
8
+ # === ���o��(<h1>, <h2>, ... , <h6>)
9
+ # �s���� ==, ===, ====, +, ++���‚��Ă����
10
+ # ���ꂼ�� H2, H3, H4, H5, H6 �ƃ^�O���‚��B
11
+ # �Ȃ��A�^�C�g����H1�^�O���g���Ă��邽�߁A= �� H1 �^�O�͂‚��Ȃ��B
12
+ # === �Q��(�����N)
13
+ # URL�Ƀ����N�𒣂�ɂ͎��̂悤�ɂ���B
14
+ # =begin
15
+ # ((<URL:http://www.ruby-land.org>)) <- ���̌`���Œ��ɏ����ꂽURL�ւ̃����N��������B
16
+ # ((<Ruby|URL:http://www.ruby-lang.org>)) <- "|"�̑O�ɕ�����������ƁA���̕����񂪕\�������B
17
+ # ((<URL:/usr/root/knowledge/ex01.knlge>)) <- Gfdnavi����URL�ւ̃����N�͂��̋L�q��OK.�\���̂��߂�URL�֎����I�ɕϊ������B
18
+ # =end
19
+ # === �ʏ�̕���
20
+ # �s�����當���������ƒʏ�̃e�L�X�g���o�͂����B<p>�^�O�ň͂܂��B
21
+ # ���s�͖�������A��s������Ɖ��i���ƂȂ�B
22
+ # === ���p���[�h
23
+ # �C���f���g���󂯂ĕ����������ƁA���p���[�h(Preformatted Text)�ƂȂ�B<pre>�^�O�ň͂܂��B
24
+ # �C���f���g�Ƃ��Ĉ�����͔̂��p�󔒂����ł���B
25
+ # === �ӏ�����
26
+ # �s���̕������A�X�^���X�N�̍s�͉ӏ������ɕϊ������B
27
+ # �C���f���g����Ɖӏ������̓���q�ɂȂ�B
28
+ # (����)�Ŏn�܂�s�͔ԍ��t�����X�g�ɂȂ�B
29
+ # === ����
30
+ # ((*����*))�̂悤�ɃA�X�^���X�N�ň͂ނƋ����\��(<em>�^�O)�ɂȂ�B
31
+ #
32
+ class RDParser
33
+ # = knowledge�h�L�������g�Ɋ܂܂��v�f�͑S��RDElement�^�Ƃ���B
34
+ # RDElement�̒��ɕ�����RDElement������B
35
+ class RDElement < Array
36
+ attr_accessor :element_type
37
+
38
+ def collect
39
+ ary = super
40
+ ctn = self.class.new(ary)
41
+ ctn.element_type = self.element_type
42
+ ctn
43
+ end
44
+
45
+ def deep_each(&block)
46
+ each do |x|
47
+ if x.is_a?(RDElement)
48
+ yield(x)
49
+ x.deep_each(&block)
50
+ else
51
+ yield(x)
52
+ end
53
+ end
54
+ end
55
+
56
+ def deep_collect(&block)
57
+ collect do |x|
58
+ if x.is_a?(RDElement)
59
+ yield(x)
60
+ x.deep_collect(&block)
61
+ else
62
+ yield(x)
63
+ end
64
+ end
65
+ end
66
+
67
+ def insert_to_tree
68
+ self[-2].push(self[-1])
69
+ self.pop
70
+ return self
71
+ end
72
+ end
73
+
74
+ def initialize(text)
75
+ @text = text
76
+ @rd_top = RDElement.new
77
+ @rd_top.element_type = ""
78
+ @aname = Hash.new
79
+ @parse_error = Array.new
80
+ @mark_indent_stack = Array.new
81
+ @text_indent_stack = Array.new
82
+ end
83
+
84
+ # �����͂ɂ��c���[�����
85
+ def make_tree
86
+ # initialize
87
+ current_container = RDElement.new
88
+ current_container.element_type = "top"
89
+ current_container = @rd_top
90
+ current_mode = String.new
91
+ leaf = RDElement.new
92
+ @mark_indent_stack = [-1]
93
+ @text_indent_stack = [-1]
94
+
95
+ @text.each_line {|line|
96
+ =begin
97
+ print "===============================\n"
98
+ print "line = "
99
+ pp line
100
+ print "@mark_indent_stack = "
101
+ pp @mark_indent_stack
102
+ print "@text_indent_stack = "
103
+ pp @text_indent_stack
104
+ =end
105
+
106
+ # "#" is comment.
107
+ next if /^#/ =~ line
108
+
109
+ # html_escape ({'&'=>'&amp;','"'=>'&quot;','>'=>'&gt;','<'=>'&lt;'})
110
+ line.gsub!(/\&/, "&amp;")
111
+ line.gsub!(/\"/, "&quot;")
112
+ line.gsub!(/</, "&lt;")
113
+ line.gsub!(/>/, "&gt;")
114
+
115
+ # = �V���ȍs���O�̍s�̑������ǂ����𒲂ׂ�
116
+ # == return String : continue -> add String to current_container
117
+ # == return nil : not continue -> new_leaf = RDElement.new\ current_container.push(new_leaf)
118
+ succeeding_line = succeession_check(current_mode, line)
119
+ if succeeding_line
120
+ current_container[-1][-1] += succeeding_line
121
+ else
122
+ case line
123
+ when /^(\+|\=)+(.*?)\r?$/ # <h1>, <h2>, ... , <h6>
124
+ new_leaf = RDElement.new([$2])
125
+ new_leaf.element_type = case line
126
+ when /^\+{2}/ then "h6"
127
+ when /^\+{1}/ then "h5"
128
+ when /^={4}/ then "h4"
129
+ when /^={3}/ then "h3"
130
+ when /^={2}/ then "h2"
131
+ when /^={1}/ then "h1"
132
+ end
133
+ mark_indent = text_indent = 0
134
+ when /^(\s*)\*(\s*)[ ]*(.*?)\r?$/ # itemize
135
+ new_leaf = RDElement.new([$3])
136
+ new_leaf.element_type = "item"
137
+ container_type = "itemize"
138
+ mark_indent = $1.length
139
+ text_indent = mark_indent + 1 + $2.length
140
+ when /^(\s*)\((\d)+\)([ ]*)(.*?)\r?$/ # enumerate
141
+ new_leaf = RDElement.new([$4])
142
+ new_leaf.element_type = "item"
143
+ container_type = "enumerate"
144
+ mark_indent = $1.length
145
+ text_indent = mark_indent + 1 + $2.length + 1 + $3.length
146
+ when /^(\s+)(.+?)\r?$/ # <pre> - </pre>
147
+ new_leaf = RDElement.new([$2 + "\n"])
148
+ new_leaf.element_type = "preformatted"
149
+ container_type = "container"
150
+ mark_indent = text_indent = $1.length
151
+ else
152
+ /^(.*?)(\r?)$/ =~ line
153
+ new_leaf = RDElement.new([$1])
154
+ new_leaf.element_type = "text"
155
+ mark_indent = text_indent = 0
156
+ end
157
+ =begin
158
+ print "current_mode = "
159
+ pp current_mode
160
+ print "new_leaf.element_type = "
161
+ pp new_leaf.element_type
162
+ =end
163
+
164
+ # ���̃��[�h��item��preformatted�Ȃ�A�܂�1up����(�C���f���g����–߂��Acurrent_container����‘O�ɕt���ւ���)
165
+ # ������item����item�Ȃ炻��͂��Ȃ�
166
+ if (current_mode == "item" && new_leaf.element_type != "item") || (current_mode == "preformatted")
167
+ current_container = @rd_top
168
+ (@mark_indent_stack.length - 1).times do
169
+ current_container = current_container[-1]
170
+ end
171
+ @mark_indent_stack.pop
172
+ @text_indent_stack.pop
173
+ end
174
+
175
+ case new_leaf.element_type
176
+ when "item", "preformatted"
177
+ case @mark_indent_stack[-1] <=> mark_indent
178
+ when 1 # "up" �C���f���g����ʂɖ߂�ꍇ
179
+ count = 0
180
+
181
+ # �ǂ̈ʒu�܂Ŗ߂邩(���K�w�߂邩)���v�Z
182
+ @mark_indent_stack.each {|m|
183
+ if m >= mark_indent
184
+ break
185
+ else # m < mark_indent
186
+ count += 1
187
+ end
188
+ }
189
+
190
+ # item(itemize, enumerate)�Ȃ��Ōv�Z�����񐔕������̂ڂ���current_container���‚�������B
191
+ # ���ꂪ�A�z���[]��‚��邱�ƂɂȂ�B
192
+ if new_leaf.element_type == "item"
193
+ current_container = @rd_top
194
+ count.times do
195
+ current_container = current_container[-1]
196
+ end
197
+ end
198
+ @mark_indent_stack = @mark_indent_stack[0..count]
199
+ @text_indent_stack = @text_indent_stack[0..count]
200
+
201
+ when -1 # "down" �C���f���g������ɐ[���Ȃ�ꍇ
202
+ # item(itemize, enumerate)�Ȃ�[���@��
203
+ if new_leaf.element_type == "item"
204
+ new_container = RDElement.new # for indent, make a new container.
205
+ new_container.element_type = container_type
206
+ current_container.push(new_container)
207
+ current_container = current_container[-1]
208
+ end
209
+ @mark_indent_stack.push(mark_indent)
210
+ @text_indent_stack.push(text_indent)
211
+ end
212
+ else # when "h1", "h2", ... , "h6", "text"
213
+ current_container = @rd_top
214
+ @mark_indent_stack = [-1]
215
+ @text_indent_stack = [-1]
216
+ end
217
+ current_container.push(new_leaf)
218
+ current_mode = new_leaf.element_type
219
+ end
220
+ }
221
+
222
+ =begin
223
+ print "==========\n"
224
+ print "==========\n"
225
+ print "@rd_top = "
226
+ pp @rd_top
227
+ =end
228
+
229
+ return @rd_top
230
+ end
231
+
232
+ # �c���[�̗v�f�����āAelement_type�ɉ����ēK�؂�HTML������
233
+ def to_html(image_paths)
234
+ @rd_top.deep_collect do |rd|
235
+ if rd.class == RDParser::RDElement
236
+ if rd[0].class == String
237
+ # ���p���[�h�ȊO�ł͎Q�Ƃ�����
238
+ unless rd.element_type == "preformatted"
239
+ # ����<em>
240
+ if /.*\(\(\*.+?\*\)\).*/ =~ rd[0]
241
+ rd[0].gsub!(/\(\(\*/, "<em class=davis>")
242
+ rd[0].gsub!(/\*\)\)/, "</em>")
243
+ end
244
+
245
+ # === �Q��(link)
246
+ # ==== �܂�((< >))�̑g�ݍ��킹�����‚���
247
+ rd[0].gsub!(/\(\(&lt;(.+?)&gt;\)\)/){|x|
248
+ # ==== | �̗L��
249
+ inner = $1
250
+ case inner
251
+ when /(.+)\|(.+)/
252
+ display = $1
253
+ link = $2
254
+ else
255
+ display = inner
256
+ link = inner
257
+ end
258
+
259
+ # ==== "URL:"�Ŏn�܂��Ă��邩�H
260
+ case link
261
+ when /^URL:(.+)/ # �O�������N
262
+ display = $1 if display == link
263
+ link = $1
264
+ when /^\/(.+)/ # �����p�X
265
+ path = $1
266
+ case path
267
+ when /^(.+)\/(.+?).knlge$/ # �m���h�L�������g
268
+ display = $2 + ".knlge"
269
+ link = "/knowledge/show?path=/#{$1}/#{$2}.knlge"
270
+ when /^(.+)\/(.+?).png$/ # png�摜
271
+ display = $2 + ".png"
272
+ link = "/image/show?path=/#{$1}/#{$2}.png"
273
+ else # ���̑�(details��\��)
274
+ link = "/description/node?path=#{link}"
275
+ # ������̓f�B���N�g�����J����悤�ɂ���
276
+ end
277
+ else
278
+ # �y�[�W�������N # not found �Ȃ�C�^���b�N�̂ŏo���悤�ɂ�����
279
+ if /^figure\s*(\d+)$/ =~ link
280
+ link = "#figure_" + $1
281
+ else
282
+ link = "#" + link
283
+ end
284
+ end
285
+ "<a href=#{link}>#{display}</a>"
286
+ }
287
+
288
+ # === �G�̖��ߍ���
289
+ # (([number. width]))
290
+ rd[0].gsub!(/\(\(\[\s*(\d+)[\s,]+(.*?)\s*\]\)\)/){|x|
291
+ img_tag = "<img src=\"/image/show?path=#{image_paths[$1.to_i - 1]}\" alt=\"Figure #{$1}\" width=#{$2}/>"
292
+ if (image = Image.find(:first, :conditions => ['path=?', image_paths[$1.to_i - 1]]))
293
+ vizshot_yaml = image.vizshot
294
+ vizshot = YAML.load(vizshot_yaml)
295
+ end
296
+ uri_params = Analysis.uri_params_from_vizshot(vizshot)
297
+ redraw_this_image = "<span title='then you can further explore the data.'>
298
+ <a href='/knowledge/fig2analysis?image_id=#{image.id}'>&lt;redraw this image&gt;</a>
299
+ </span>"
300
+ get_the_url = "<span title='Get the URL to redraw this image.'>
301
+ <a href='/analysis/execute?#{uri_params}'>&lt;Get the URL&gt;</a>
302
+ </span>"
303
+
304
+ if (image)
305
+ if (uri_params)
306
+ # ���ߍ��ސ}���������ꍇ���l�����āA<redraw �`>��<get the URL>�̊Ԃ�<br>�^�O���͂���
307
+ img_tag + "<br>" + redraw_this_image + "<br>" + get_the_url
308
+ else
309
+ # Gfdnavi�O�ō��ꂽ�G�̏ꍇ�͉摜�t�@�C���̂ݕ\������
310
+ img_tag
311
+ end
312
+ else
313
+ "<img src='x.gif'>Image not found."
314
+ end
315
+ }
316
+ end
317
+ end
318
+
319
+ case rd.element_type
320
+ when /^h(\d)$/
321
+ # <h1>�p��if��
322
+ # <h1>�̓^�C�g���p�A�{���ɂ͎g�p�֎~
323
+ if ($1.to_i == 1)
324
+ rd[0] = "<h2 id=\"#{rd[0]}\" class=davis>" + rd[0] + "</h2>\n" + "&nbsp;&nbsp;<font color ='red'>= is disabled because &lt;h1&gt; tag is used for title.</font>"
325
+ else
326
+ rd[0] = "<h#{$1} id=\"#{rd[0]}\" class=davis>" + rd[0] + "</h#{$1}>\n"
327
+ end
328
+ when "preformatted"
329
+ rd[0] = "<pre class=davis>" + rd[0] + "</pre>\n"
330
+ when "itemize"
331
+ ul1 = RDElement.new(["<ul class=davis>"])
332
+ ul1.element_type = "ul1"
333
+ ul2 = RDElement.new(["</ul>"])
334
+ ul2.element_type = "ul2"
335
+ rd.insert(0, ul1).push(ul2)
336
+ when "enumerate"
337
+ ol1 = RDElement.new(["<ol class=davis>"])
338
+ ol1.element_type = "ol1"
339
+ ol2 = RDElement.new(["</ol>"])
340
+ ol2.element_type = "ol2"
341
+ rd.insert(0, ol1).push(ol2)
342
+ when "item" then rd[0] = "<li class=davis>" + rd[0].to_s + "</li>\n"
343
+ when "text" then rd[0] = "<p class=davis>" + rd[0].to_s + "</p>\n" unless rd[0] == ""
344
+ end
345
+ end
346
+ end
347
+ return @rd_top
348
+ end
349
+
350
+ private
351
+ # check that line is the succeeding phrase as previous line or not.
352
+ ## return String : continue -> add String to current_container
353
+ ## return nil : not continue -> new_leaf = RDElement.new\ current_container.push(new_leaf)
354
+ def succeession_check(current_mode, line)
355
+ case current_mode
356
+ when "text" # �s����+,=,*, ,(1)�A�������͋�s�Ȃ�p�����Ȃ�
357
+ return case line
358
+ when /^(=|\+|\*|\s|\(\d+\))/ then nil
359
+ when /^(.*?)\r?$/ then $1
360
+ else line
361
+ end
362
+ when "item"
363
+ # �擪����󔒂������A
364
+ # ���͕����̃C���f���g�̐�����v����Όp��
365
+ # h1, h2, ... , itemize, enumerate �ɂȂ�Ȃ�p�����Ȃ�
366
+ unless ((/^(\+|\=)/ =~ line) || (/^[ ]*(\*|\(\d+\))/ =~ line))
367
+ if (/^([ ]*)(.*?)([\r]*)$/ =~ line)
368
+ spaces = $1.length
369
+ linebody = $2
370
+ return linebody if (spaces == @text_indent_stack[-1])
371
+ end
372
+ end
373
+ when "preformatted"
374
+ case line
375
+ when /^([ ]*?)[\r]*$/ # ��s�̏ꍇ�͋�s�����̂܂܏o��
376
+ return "\n"
377
+ when /^([ ]+)(.*?)[\r]*$/ # �s�����󔒂Ȃ�
378
+ diff = $1.length - @text_indent_stack[-1] # indent = $1.length
379
+ return case
380
+ when diff > 0 : " " * diff + $2 + "\n" # �C���f���g���������炻�̕��̋󔒂�����
381
+ when diff < 0 : nil # �C���f���g���߂�Όp�����Ȃ�
382
+ else $2 + "\n"
383
+ end
384
+ else # �s�����󔒂Ŗ�����Όp�����Ȃ�
385
+ return nil
386
+ end
387
+ else # current_type��nil�̂Ƃ��A�܂���<h1>-<h6>�̂Ƃ��͌p�����Ȃ�
388
+ return nil
389
+ end
390
+ end
391
+
392
+ end