| 778edd6 | Dane Bell | 02 August 2016, 21:40:32 UTC | Tests for issue 259 | 02 August 2016, 21:40:32 UTC |
| 44ab46f | Tom Hicks | 01 August 2016, 22:23:07 UTC | Merge pull request #298 from clulab/precedence-tweaks | 01 August 2016, 22:23:07 UTC |
| 9e0a75f | Tom Hicks | 01 August 2016, 15:37:40 UTC | Update build file to use released bioresources 1.1.14. | 01 August 2016, 15:37:40 UTC |
| dae94ec | Tom Hicks | 01 August 2016, 15:36:38 UTC | Update for NER corrections in BioResources 1.1.4. | 01 August 2016, 15:36:38 UTC |
| bec05fb | Tom Hicks | 31 July 2016, 02:20:31 UTC | Minor tweak to trace message. Update last modified doc string. | 31 July 2016, 02:20:31 UTC |
| b02c4ba | Gus Hahn-Powell | 30 July 2016, 07:03:12 UTC | Fixed mkAssemblyModifications | 30 July 2016, 07:03:12 UTC |
| 65cc984 | Gus Hahn-Powell | 30 July 2016, 06:53:55 UTC | Assembly TODOs | 30 July 2016, 06:57:19 UTC |
| eeb4d1d | Gus Hahn-Powell | 30 July 2016, 06:45:47 UTC | Clean up assembly tests | 30 July 2016, 06:45:47 UTC |
| eec44d8 | Gus Hahn-Powell | 30 July 2016, 01:35:53 UTC | Don't include EER in its own predecessors the eer will end up in the predecessors because of the breadcrumbs used to avoid causal precedence loops. | 30 July 2016, 01:36:08 UTC |
| 75c3157 | Gus Hahn-Powell | 30 July 2016, 01:34:38 UTC | Be conservative when establishing precedence Previously, a precedence relation was mapped to equivalent EERs. | 30 July 2016, 01:34:38 UTC |
| 3118283 | Tom Hicks | 29 July 2016, 22:38:57 UTC | Merge pull request #297 from clulab/breadcrumb-predecessors Breadcrumb predecessors (resolves #296) | 29 July 2016, 22:38:57 UTC |
| 37318c3 | Gus Hahn-Powell | 29 July 2016, 21:47:19 UTC | Remove outputType | 29 July 2016, 21:47:19 UTC |
| 4c54946 | Gus Hahn-Powell | 29 July 2016, 21:45:56 UTC | Correct logging directory | 29 July 2016, 21:45:56 UTC |
| 121a7a6 | Mihai Surdeanu | 29 July 2016, 21:24:27 UTC | Merge pull request #295 from clulab/feedback2 Feedback2 | 29 July 2016, 21:24:27 UTC |
| 54a66b7 | Gus Hahn-Powell | 29 July 2016, 21:20:13 UTC | Resolves #296 TestReachCLI suite passes with BR 1.1.14-SNAPSHOT | 29 July 2016, 21:20:13 UTC |
| 6c479c4 | Gus Hahn-Powell | 29 July 2016, 20:48:37 UTC | Use bioresources 1.1.14-SNAPSHOT | 29 July 2016, 20:48:37 UTC |
| 5ffff9f | Gus Hahn-Powell | 29 July 2016, 20:36:37 UTC | Keep track of what predecessors have been seen | 29 July 2016, 20:48:26 UTC |
| 2420922 | Gus Hahn-Powell | 29 July 2016, 20:36:28 UTC | Removed empty line | 29 July 2016, 20:36:28 UTC |
| 9ac7afd | Dane Bell | 29 July 2016, 19:36:54 UTC | Comment out extraneous rule | 29 July 2016, 19:36:54 UTC |
| 8cb2e60 | Dane Bell | 29 July 2016, 18:51:50 UTC | Merge branch 'master' into feedback2 | 29 July 2016, 18:51:50 UTC |
| 82f0e7b | Mihai Surdeanu | 29 July 2016, 08:23:36 UTC | Merge pull request #294 from clulab/cleanup Cleanup | 29 July 2016, 08:23:36 UTC |
| dd92da9 | Gus Hahn-Powell | 29 July 2016, 06:19:05 UTC | Updated README | 29 July 2016, 06:19:05 UTC |
| e3c4b52 | Gus Hahn-Powell | 29 July 2016, 05:57:36 UTC | Ignore sections when processing .csv/.tsv files | 29 July 2016, 05:57:36 UTC |
| 6a2fcb9 | Gus Hahn-Powell | 29 July 2016, 05:57:08 UTC | Name boolean parameters | 29 July 2016, 05:57:08 UTC |
| f750018 | Gus Hahn-Powell | 29 July 2016, 05:56:07 UTC | Cleanup | 29 July 2016, 05:56:18 UTC |
| 5029606 | Gus Hahn-Powell | 29 July 2016, 05:54:45 UTC | !_.isEmpty => _.nonEmpty | 29 July 2016, 05:54:45 UTC |
| 71b22e9 | Gus Hahn-Powell | 29 July 2016, 05:52:19 UTC | Removed redundant collection conversions | 29 July 2016, 05:52:19 UTC |
| 75f356b | Gus Hahn-Powell | 29 July 2016, 05:47:19 UTC | Test cleanup - Named boolean parameters - Removed unused imports - ! .isEmpty => .nonEmpty | 29 July 2016, 05:47:19 UTC |
| 7b303c3 | Gus Hahn-Powell | 29 July 2016, 02:08:14 UTC | Refactoring changes - ReachCLI now supports multiple outputs - Assembly can be optionally perfomed by ReachCLI - Added test for FRIES output + assembly - Removed unused DarpaFlow - Removed RunNxml2Fries (same functionality provided by ReachCLI) - Created darpa package for DARPA-specific code - nxml/indexer -> indexer - nxml/FriesEntry -> reach/FriesEntry | 29 July 2016, 05:46:59 UTC |
| 55b7f40 | Tom Hicks | 28 July 2016, 22:53:24 UTC | Merge pull request #293 from clulab/process-dsv-or-nxml Resolves #290 | 28 July 2016, 22:53:24 UTC |
| 09f2469 | Gus Hahn-Powell | 28 July 2016, 21:06:23 UTC | Resolves #290 | 28 July 2016, 21:06:23 UTC |
| ce7192e | Gus Hahn-Powell | 28 July 2016, 21:02:31 UTC | Merge pull request #292 from clulab/participant-features Add FRIES formatter output for participant features | 28 July 2016, 21:02:31 UTC |
| d9ee92c | Tom Hicks | 28 July 2016, 20:05:16 UTC | Merge latest 'master' into participant-features | 28 July 2016, 20:05:16 UTC |
| 1c0c256 | Tom Hicks | 28 July 2016, 19:35:51 UTC | Add method to get input features by participants. | 28 July 2016, 19:35:51 UTC |
| 2bea12b | Tom Hicks | 28 July 2016, 19:35:32 UTC | Move participant features to arguments, cleanup. | 28 July 2016, 19:35:32 UTC |
| f4a7dd7 | Mihai Surdeanu | 28 July 2016, 14:31:48 UTC | Merge pull request #289 from clulab/participant-features Add participant features from precedence | 28 July 2016, 14:31:48 UTC |
| c069fa7 | Gus Hahn-Powell | 28 July 2016, 05:51:31 UTC | use named args | 28 July 2016, 05:51:31 UTC |
| e27f2ff | Gus Hahn-Powell | 28 July 2016, 05:49:14 UTC | Handle all events with a single case Closes #178 | 28 July 2016, 05:49:14 UTC |
| 50cfab9 | Dane Bell | 27 July 2016, 23:32:55 UTC | Restore functionality of issue250 | 27 July 2016, 23:32:55 UTC |
| 4bfd613 | Tom Hicks | 27 July 2016, 22:36:36 UTC | Merge latest 'master' into participant-features. | 27 July 2016, 22:36:36 UTC |
| ecfa03f | Tom Hicks | 27 July 2016, 22:35:57 UTC | Comment out debugging println. | 27 July 2016, 22:35:57 UTC |
| 6b46dd8 | Tom Hicks | 27 July 2016, 22:30:20 UTC | Merge pull request #287 from clulab/complexwith2 handle n-ary bindings | 27 July 2016, 22:30:20 UTC |
| a2530fd | Tom Hicks | 27 July 2016, 22:25:42 UTC | Merge pull request #288 from clulab/issue284 Issue284 | 27 July 2016, 22:25:42 UTC |
| 72c359f | Marco Antonio Valenzuela Escárcega | 27 July 2016, 21:41:58 UTC | missing bracket | 27 July 2016, 21:41:58 UTC |
| 224e8e1 | Marco Antonio Valenzuela Escárcega | 27 July 2016, 21:38:07 UTC | use PMC as chunkId | 27 July 2016, 21:38:07 UTC |
| 61fb6b7 | Marco Antonio Valenzuela Escárcega | 27 July 2016, 21:35:39 UTC | upgrade dependencies | 27 July 2016, 21:35:39 UTC |
| b28dd7e | Marco Antonio Valenzuela Escárcega | 27 July 2016, 19:57:29 UTC | Merge branch 'master' into complexwith2 | 27 July 2016, 19:57:29 UTC |
| c28c2b3 | Gus Hahn-Powell | 27 July 2016, 08:32:16 UTC | processors 5.9.2 => 5.9.3 | 27 July 2016, 08:32:16 UTC |
| 24b7fbc | Gus Hahn-Powell | 27 July 2016, 07:25:30 UTC | Refactor for consistency | 27 July 2016, 08:15:06 UTC |
| e3ae9bd | Mihai Surdeanu | 27 July 2016, 07:43:07 UTC | Updated to processors 5.9.3 | 27 July 2016, 07:43:07 UTC |
| 7a3caa4 | Mihai Surdeanu | 27 July 2016, 07:08:21 UTC | Merge branch 'master' into feedback2 | 27 July 2016, 07:08:21 UTC |
| a5c435a | Gus Hahn-Powell | 27 July 2016, 05:50:19 UTC | Merge pull request #269 from clulab/issue250 Issue250 | 27 July 2016, 05:50:19 UTC |
| 3a52d4b | Tom Hicks | 27 July 2016, 04:25:46 UTC | First cut at adding participant features to FRIES output. | 27 July 2016, 04:25:46 UTC |
| 25bf338 | Dane Bell | 27 July 2016, 01:31:21 UTC | Fixing details | 27 July 2016, 01:31:21 UTC |
| 1029f6f | Dane Bell | 26 July 2016, 21:21:09 UTC | Merge branch 'master' into issue250 | 26 July 2016, 21:21:09 UTC |
| a61d763 | Gus Hahn-Powell | 26 July 2016, 21:13:49 UTC | Merge branch 'participant-features' of github.com:clulab/reach into participant-features | 26 July 2016, 21:13:49 UTC |
| 22badf1 | Gus Hahn-Powell | 26 July 2016, 21:13:02 UTC | Added pointer to participant's parent (Mention) | 26 July 2016, 21:13:02 UTC |
| a076990 | Dane Bell | 26 July 2016, 21:09:01 UTC | Better import erased by merge | 26 July 2016, 21:09:01 UTC |
| 385e658 | Tom Hicks | 26 July 2016, 21:03:28 UTC | Merge pull request #282 from clulab/issue268 Issue268 | 26 July 2016, 21:03:28 UTC |
| f218798 | Dane Bell | 26 July 2016, 21:02:23 UTC | Merge branch 'master' into issue250 | 26 July 2016, 21:02:23 UTC |
| a2b7b32 | marcovzla | 26 July 2016, 21:01:55 UTC | Merge pull request #283 from clulab/testclean Cleanup scalatest syntax for tests touched by issue 274. | 26 July 2016, 21:01:55 UTC |
| da4a3d1 | Dane Bell | 26 July 2016, 20:59:51 UTC | Next step in improving 'in response to' events | 26 July 2016, 20:59:51 UTC |
| a37c808 | Tom Hicks | 26 July 2016, 20:59:22 UTC | Merge latest 'master' into participant-features | 26 July 2016, 20:59:22 UTC |
| d0e9907 | Gus Hahn-Powell | 26 July 2016, 20:53:48 UTC | Assembler gets "flattened" mentions Because "flattening" incurs a loss of information, it is imperative that assembly receive the same transformed data for consistency (otherwise events will be missing from the AssemblyManager) | 26 July 2016, 20:53:48 UTC |
| d05a873 | Gus Hahn-Powell | 26 July 2016, 20:52:15 UTC | Added tracker for participant features Produces the set union of PTMs for a participant (at event input), based on the relevant features gleaned from the event's causal predecessors. | 26 July 2016, 20:52:32 UTC |
| 449e111 | Tom Hicks | 26 July 2016, 19:40:43 UTC | Cleanup scalatest syntax. | 26 July 2016, 19:40:43 UTC |
| be1cbfd | Tom Hicks | 26 July 2016, 18:08:26 UTC | Merge pull request #281 from clulab/iss274 Iss274 | 26 July 2016, 18:08:26 UTC |
| a0d873a | Marco Antonio Valenzuela Escárcega | 26 July 2016, 17:56:48 UTC | added unittest for issue268 | 26 July 2016, 17:56:48 UTC |
| 2283286 | Tom Hicks | 26 July 2016, 14:29:40 UTC | Merge relevant fix from GHPs ner-hot-mess branch. | 26 July 2016, 14:29:40 UTC |
| c4564aa | Tom Hicks | 26 July 2016, 13:55:04 UTC | Merge latest 'master' into iss274. | 26 July 2016, 13:55:04 UTC |
| c684c9d | Mihai Surdeanu | 26 July 2016, 10:09:35 UTC | Merge branch 'master' into feedback2 | 26 July 2016, 10:09:35 UTC |
| a3dad39 | Mihai Surdeanu | 26 July 2016, 10:06:42 UTC | Added more reg/act patterns and tests. | 26 July 2016, 10:06:42 UTC |
| 0e77c58 | Mihai Surdeanu | 26 July 2016, 08:11:03 UTC | Merge pull request #280 from clulab/feedback-s5s6 Addresses TestFeedback2 s5 & s6 | 26 July 2016, 08:11:03 UTC |
| 18f9bcb | Gus Hahn-Powell | 26 July 2016, 07:32:51 UTC | Quit yer yappin! | 26 July 2016, 07:32:51 UTC |
| b15e62b | Gus Hahn-Powell | 26 July 2016, 07:32:22 UTC | Resolves TestFeedback2 s5 & s6 | 26 July 2016, 07:32:22 UTC |
| ec8a1eb | Gus Hahn-Powell | 26 July 2016, 07:32:06 UTC | More TestUtils | 26 July 2016, 07:32:06 UTC |
| b29c9f8 | Gus Hahn-Powell | 26 July 2016, 07:30:57 UTC | Added filters for output Ex. remove Mentions with label Generic_* | 26 July 2016, 07:31:30 UTC |
| bd1114d | Gus Hahn-Powell | 26 July 2016, 07:30:04 UTC | Convenience method | 26 July 2016, 07:30:04 UTC |
| d658e3e | Gus Hahn-Powell | 26 July 2016, 07:28:28 UTC | Rule tweak | 26 July 2016, 07:28:28 UTC |
| 9d8fd3d | Tom Hicks | 26 July 2016, 04:36:07 UTC | Merge pull request #278 from clulab/RemovePandasOutput Removed PandasOutput.scala | 26 July 2016, 04:36:07 UTC |
| f2e5bd0 | Tom Hicks | 26 July 2016, 04:33:34 UTC | Comment out debugging statement. | 26 July 2016, 04:33:34 UTC |
| f20f6d3 | enoriega | 25 July 2016, 23:45:27 UTC | Removed PandasOutput.scala | 25 July 2016, 23:45:27 UTC |
| ee8f29d | Marco Antonio Valenzuela Escárcega | 25 July 2016, 21:45:47 UTC | changed binding3wrong for a safer version | 25 July 2016, 21:45:47 UTC |
| 17231f4 | Gus Hahn-Powell | 25 July 2016, 21:43:13 UTC | Intersection constraint should be on CONTROLLED | 25 July 2016, 21:43:13 UTC |
| 4e71eca | Gus Hahn-Powell | 25 July 2016, 21:42:33 UTC | preferSimpleEvent -> preferEvent (for controllers) | 25 July 2016, 21:42:33 UTC |
| 59fa44e | Gus Hahn-Powell | 25 July 2016, 21:42:06 UTC | Rule tweak | 25 July 2016, 21:42:06 UTC |
| a6b0714 | Gus Hahn-Powell | 25 July 2016, 21:01:38 UTC | Fixed rules | 25 July 2016, 21:01:38 UTC |
| 6bb0152 | Marco Antonio Valenzuela Escárcega | 25 July 2016, 20:36:03 UTC | added binding test | 25 July 2016, 20:36:03 UTC |
| d43e4e1 | Gus Hahn-Powell | 25 July 2016, 20:06:39 UTC | Added two new rules | 25 July 2016, 20:06:39 UTC |
| fce020b | Marco Antonio Valenzuela Escárcega | 25 July 2016, 19:41:45 UTC | handle n-ary bindings | 25 July 2016, 19:41:45 UTC |
| c044ec0 | Tom Hicks | 25 July 2016, 15:16:40 UTC | Add tests for Reach issue #274 (NB: correct grounding still fails in one test). | 25 July 2016, 15:16:40 UTC |
| 4816f13 | Tom Hicks | 25 July 2016, 14:38:27 UTC | Add tests for Reach issue #274. | 25 July 2016, 14:38:27 UTC |
| db53824 | Tom Hicks | 25 July 2016, 14:03:20 UTC | Remove unused import. | 25 July 2016, 14:03:20 UTC |
| 09c9425 | Tom Hicks | 25 July 2016, 13:54:03 UTC | Reactivate test after fix of Processors issue #61. | 25 July 2016, 13:54:03 UTC |
| c3b7715 | Mihai Surdeanu | 25 July 2016, 11:53:14 UTC | Added more reg/act patterns. A few reg tests currently fail. | 25 July 2016, 11:53:14 UTC |
| 7bba72f | Mihai Surdeanu | 24 July 2016, 06:32:03 UTC | Merge pull request #276 from clulab/release Added plugins to help with the release process. | 24 July 2016, 06:32:03 UTC |
| bedb03d | Marco Antonio Valenzuela Escárcega | 24 July 2016, 02:11:15 UTC | use sbt-release | 24 July 2016, 02:11:15 UTC |
| a32a3ef | Mihai Surdeanu | 22 July 2016, 06:42:06 UTC | Merge pull request #273 from clulab/Issue257 Issue 257 | 22 July 2016, 06:42:06 UTC |
| 79aca9a | enoriega | 21 July 2016, 21:45:17 UTC | Passes the test and adds active voice for translocations | 21 July 2016, 21:45:17 UTC |
| d4b75c7 | Dane Bell | 21 July 2016, 20:57:49 UTC | Improve site detection re overlap with mutation | 21 July 2016, 20:57:49 UTC |
