| db7a1c7 | Tom Hicks | 30 August 2016, 00:36:43 UTC | Merge latest 'master' into dsv-parser-encoding | 30 August 2016, 00:36:43 UTC |
| 6097513 | Tom Hicks | 29 August 2016, 23:54:41 UTC | Merge pull request #333 from clulab/assembly-tsv-fix Remove illicit whitespace chars from output | 29 August 2016, 23:54:41 UTC |
| eb297e2 | Gus Hahn-Powell | 29 August 2016, 22:26:17 UTC | Remove illicit whitespace chars from output | 29 August 2016, 22:26:17 UTC |
| 96b544f | Mihai Surdeanu | 26 August 2016, 16:02:53 UTC | Close io.Source all the time! | 26 August 2016, 16:02:53 UTC |
| 8187caa | Mihai Surdeanu | 25 August 2016, 21:33:36 UTC | Handle NXML errors robustly | 25 August 2016, 21:33:36 UTC |
| 617251b | Mihai Surdeanu | 25 August 2016, 21:17:11 UTC | Added indexing for pub year to NxmlIndexer | 25 August 2016, 21:17:11 UTC |
| 3b4424c | Gus Hahn-Powell | 25 August 2016, 21:02:54 UTC | Handle wonky encodings | 25 August 2016, 21:02:54 UTC |
| 3865344 | Mihai Surdeanu | 24 August 2016, 21:41:03 UTC | Merge pull request #329 from clulab/nxmlindexer Add hoc solution to text preprocessing for the nxml indexer | 24 August 2016, 21:41:03 UTC |
| ef617a0 | Enrique Noriega | 24 August 2016, 21:36:27 UTC | Pending comments | 24 August 2016, 21:36:27 UTC |
| 07c28df | Enrique Noriega | 24 August 2016, 21:35:40 UTC | Pending comments | 24 August 2016, 21:35:40 UTC |
| 54e09cf | Enrique Noriega | 24 August 2016, 21:22:20 UTC | Add hoc solution to text preprocessing for the nxml indexer | 24 August 2016, 21:22:20 UTC |
| 86ddb11 | Mihai Surdeanu | 23 August 2016, 22:36:34 UTC | Added the TB use case. | 23 August 2016, 22:36:34 UTC |
| 59d4785 | Tom Hicks | 21 August 2016, 22:20:28 UTC | Merge pull request #323 from clulab/issue314 Update build to use ai.lum 0.0.6: fixes NXML reader problems. | 21 August 2016, 22:20:28 UTC |
| ec7d754 | Tom Hicks | 21 August 2016, 21:06:54 UTC | Update build to use ai.lum 0.0.6: fixes NXML reader problems. | 21 August 2016, 21:06:54 UTC |
| d230c10 | Mihai Surdeanu | 19 August 2016, 12:10:22 UTC | Merge pull request #320 from clulab/hansbug Hansbug | 19 August 2016, 12:10:22 UTC |
| 749cd34 | Tom Hicks | 19 August 2016, 10:40:59 UTC | Merge latest 'master' into hansbug | 19 August 2016, 10:40:59 UTC |
| ebebbdc | Tom Hicks | 19 August 2016, 10:21:26 UTC | Rewrite order dependent tests of FRIES outputter. | 19 August 2016, 10:21:26 UTC |
| dfb7acf | Gus Hahn-Powell | 19 August 2016, 04:45:05 UTC | Don't add event's args to top-level frame list | 19 August 2016, 04:45:05 UTC |
| 42f2801 | Gus Hahn-Powell | 19 August 2016, 04:33:14 UTC | check eventsDone | 19 August 2016, 04:33:14 UTC |
| 90c8e3a | Tom Hicks | 19 August 2016, 01:17:12 UTC | Sort mention maps by sentence order. Undo event id. | 19 August 2016, 01:17:12 UTC |
| 792098d | Tom Hicks | 18 August 2016, 23:42:31 UTC | Cleanups. | 18 August 2016, 23:42:31 UTC |
| 01b8cc0 | Gus Hahn-Powell | 18 August 2016, 22:34:38 UTC | Used EMaps for model output | 18 August 2016, 22:34:38 UTC |
| 2b99cd5 | Tom Hicks | 18 August 2016, 19:09:42 UTC | Handle event and relation mentions together. | 18 August 2016, 19:09:42 UTC |
| bd2690c | Gus Hahn-Powell | 18 August 2016, 18:13:51 UTC | Don't need BioMentions | 18 August 2016, 18:13:51 UTC |
| ab1d025 | Gus Hahn-Powell | 18 August 2016, 17:54:58 UTC | .toBioMention fix | 18 August 2016, 17:54:58 UTC |
| c8b5897 | Gus Hahn-Powell | 18 August 2016, 17:45:23 UTC | Merge branch 'hansbug' of github.com:clulab/reach into hansbug | 18 August 2016, 17:45:23 UTC |
| 355995b | Gus Hahn-Powell | 18 August 2016, 17:44:32 UTC | Use processors v5.9.4 | 18 August 2016, 17:44:32 UTC |
| 57bb34b | Tom Hicks | 18 August 2016, 17:44:06 UTC | Update build file to match master and use processors 5.9.4. | 18 August 2016, 17:44:06 UTC |
| aeca369 | Gus Hahn-Powell | 18 August 2016, 17:43:43 UTC | Use generic procedure for populating EMaps | 18 August 2016, 17:43:43 UTC |
| 647aad7 | Gus Hahn-Powell | 18 August 2016, 17:37:35 UTC | Changes to mkMapEntries mk -> make Take a Seq[BioMention] | 18 August 2016, 17:37:35 UTC |
| 51d6346 | Gus Hahn-Powell | 18 August 2016, 17:26:53 UTC | mkEventId -> mkEntityId | 18 August 2016, 17:26:53 UTC |
| cf192d0 | Gus Hahn-Powell | 18 August 2016, 17:16:57 UTC | More generic method for populating maps currently unused, but designed to merge mkEntityMapEntry and mkEventMapEntry | 18 August 2016, 17:16:57 UTC |
| 166e5d1 | Gus Hahn-Powell | 18 August 2016, 17:16:18 UTC | Handle args of a Complex | 18 August 2016, 17:16:18 UTC |
| 404ca18 | Tom Hicks | 18 August 2016, 01:07:03 UTC | Update to use Processors 5.9.4. Update CHANGES file. | 18 August 2016, 01:07:03 UTC |
| 3777e05 | Tom Hicks | 17 August 2016, 22:48:09 UTC | Fix first failing test as a test of fix. | 17 August 2016, 22:48:09 UTC |
| a63b210 | Tom Hicks | 17 August 2016, 13:03:43 UTC | Recursively process relation mention arguments of nested events. | 17 August 2016, 13:03:43 UTC |
| 388d352 | Tom Hicks | 17 August 2016, 09:44:02 UTC | Recursively process arguments of nested events. | 17 August 2016, 09:44:02 UTC |
| 4bd4be0 | Tom Hicks | 17 August 2016, 07:10:29 UTC | Better argument processing loop in makeEventMention. | 17 August 2016, 07:10:29 UTC |
| 29983fc | Tom Hicks | 16 August 2016, 19:41:48 UTC | Merge pull request #319 from clulab/issue317 Issue317 | 16 August 2016, 19:41:48 UTC |
| 6127d05 | Gus Hahn-Powell | 16 August 2016, 19:09:51 UTC | AssemblyRunner.XXX -> Assembler.XXX | 16 August 2016, 19:09:51 UTC |
| 65b9b2a | Gus Hahn-Powell | 16 August 2016, 18:52:05 UTC | Reverted processors dependency | 16 August 2016, 18:52:05 UTC |
| fa60627 | Gus Hahn-Powell | 16 August 2016, 18:46:57 UTC | Added memoization of predecessors. Resolves #317 | 16 August 2016, 18:46:57 UTC |
| 2f62990 | Gus Hahn-Powell | 16 August 2016, 18:45:40 UTC | No need for new (Assembler is not a case class) | 16 August 2016, 18:45:40 UTC |
| a56bd79 | Gus Hahn-Powell | 16 August 2016, 18:44:34 UTC | Serialization methods and alternative constructor | 16 August 2016, 18:44:34 UTC |
| af20966 | Gus Hahn-Powell | 16 August 2016, 18:40:13 UTC | Added getMentions method | 16 August 2016, 18:40:13 UTC |
| 7d91cf2 | Gus Hahn-Powell | 16 August 2016, 18:39:44 UTC | saveTo/LoadFrom methods for serialization | 16 August 2016, 18:39:44 UTC |
| c59ba17 | Gus Hahn-Powell | 16 August 2016, 18:34:50 UTC | Alternatively get Entry from filename (String) | 16 August 2016, 18:35:08 UTC |
| 9416122 | Gus Hahn-Powell | 16 August 2016, 18:33:57 UTC | Postpone loading of ReachSystem in PaperReader | 16 August 2016, 18:34:31 UTC |
| bb3d88a | Gus Hahn-Powell | 16 August 2016, 18:31:50 UTC | Moved sieve ordering to Assembler object | 16 August 2016, 18:32:05 UTC |
| a805360 | Mihai Surdeanu | 16 August 2016, 15:52:43 UTC | Merge pull request #318 from clulab/sane-logging Added functioning logger | 16 August 2016, 15:52:43 UTC |
| d869f33 | Gus Hahn-Powell | 16 August 2016, 14:08:49 UTC | Added functioning logger Properties defined in logback.xml are configurable via application.conf | 16 August 2016, 14:08:49 UTC |
| dd8c6c5 | Tom Hicks | 11 August 2016, 16:16:02 UTC | Merge pull request #315 from clulab/nfo Rewrite of FriesOutput | 11 August 2016, 16:16:02 UTC |
| 23667e6 | Tom Hicks | 10 August 2016, 20:01:54 UTC | Minor cleanups. | 10 August 2016, 20:01:54 UTC |
| c78a257 | Tom Hicks | 10 August 2016, 18:34:55 UTC | Replace old fries outputter. | 10 August 2016, 18:34:55 UTC |
| f10a59b | Tom Hicks | 10 August 2016, 18:33:42 UTC | Update for flattened controllers. | 10 August 2016, 18:33:42 UTC |
| 2da94e0 | Tom Hicks | 10 August 2016, 08:02:27 UTC | Revamp make argument method. More cleanups. | 10 August 2016, 08:02:27 UTC |
| dbd0e48 | Tom Hicks | 09 August 2016, 20:19:00 UTC | Revamp event argument processing. Continue cleaning. | 09 August 2016, 20:19:00 UTC |
| a7c5fc1 | Tom Hicks | 09 August 2016, 08:45:29 UTC | Continue revamping. | 09 August 2016, 08:45:29 UTC |
| fe9d3ec | Tom Hicks | 09 August 2016, 02:09:27 UTC | Initial changes for entities. | 09 August 2016, 02:09:27 UTC |
| ea47f17 | Tom Hicks | 05 August 2016, 09:10:20 UTC | Merge pull request #313 from clulab/nxml upgrade nxmlreader | 05 August 2016, 09:10:20 UTC |
| 8b026d2 | Marco Antonio Valenzuela Escárcega | 05 August 2016, 02:27:55 UTC | upgrade nxmlreader | 05 August 2016, 02:27:55 UTC |
| 37e8167 | Tom Hicks | 04 August 2016, 23:16:46 UTC | Merge pull request #312 from clulab/assembly-empty-iterator-bug Solves empty iterator bug | 04 August 2016, 23:16:46 UTC |
| e0d053d | Tom Hicks | 04 August 2016, 22:45:23 UTC | Merge pull request #311 from clulab/mention-filter-bug solves the "key not found: controller" encountered in the 1K | 04 August 2016, 22:45:23 UTC |
| 8dc3696 | Gus Hahn-Powell | 04 August 2016, 22:14:04 UTC | fixes "key not found: controller" | 04 August 2016, 22:14:04 UTC |
| 2d4694e | Tom Hicks | 04 August 2016, 20:00:23 UTC | Merge pull request #310 from clulab/nxmlreader upgrade nxmlreader | 04 August 2016, 20:00:23 UTC |
| cd96b97 | Gus Hahn-Powell | 04 August 2016, 19:17:08 UTC | Check if mentions being compared have controllers | 04 August 2016, 19:17:08 UTC |
| 1e69da3 | Gus Hahn-Powell | 04 August 2016, 18:43:44 UTC | Solves empty iterator bug - encountered in PMC3365374 and PMC3365593 | 04 August 2016, 18:43:44 UTC |
| fcf5bfa | Marco Antonio Valenzuela Escárcega | 04 August 2016, 18:25:57 UTC | upgrade nxmlreader | 04 August 2016, 18:25:57 UTC |
| 764bab3 | Tom Hicks | 03 August 2016, 20:37:52 UTC | Merge pull request #307 from clulab/degrade-binding-controllers Added more tests for degradation of output | 03 August 2016, 20:37:52 UTC |
| 592f8e4 | Tom Hicks | 03 August 2016, 20:07:11 UTC | Test now passing. | 03 August 2016, 20:07:11 UTC |
| 8ef232b | Gus Hahn-Powell | 03 August 2016, 19:11:19 UTC | Added more tests for degradation of output | 03 August 2016, 19:11:19 UTC |
| 081c318 | Tom Hicks | 03 August 2016, 00:17:30 UTC | Merge pull request #305 from clulab/issue259 Issue259 | 03 August 2016, 00:17:30 UTC |
| a156819 | Dane Bell | 02 August 2016, 23:44:12 UTC | Repair modification trigger finding | 02 August 2016, 23:44:12 UTC |
| 8a74a91 | Dane Bell | 02 August 2016, 23:16:18 UTC | Avoid warnings in bioprocessValid | 02 August 2016, 23:16:18 UTC |
| dc5db17 | Dane Bell | 02 August 2016, 23:15:49 UTC | Merge branch 'master' into issue259 | 02 August 2016, 23:15:49 UTC |
| 7fa0929 | Tom Hicks | 02 August 2016, 22:21:10 UTC | Merge pull request #304 from clulab/leaner-features Don't use trigrams in feature extractor for causal precedence classifier | 02 August 2016, 22:21:10 UTC |
| 4e6ce04 | Tom Hicks | 02 August 2016, 21:58:51 UTC | Merge pull request #303 from clulab/n-complex Turn n-ary complex into n-ary binding event | 02 August 2016, 21:58:51 UTC |
| 0233915 | Dane Bell | 02 August 2016, 21:47:21 UTC | Also change _syntax_1b_verb rule just like _syntax_1a_verb | 02 August 2016, 21:47:21 UTC |
| b909050 | Dane Bell | 02 August 2016, 21:40:57 UTC | Slight adjustments to cover issue 259 | 02 August 2016, 21:40:57 UTC |
| 778edd6 | Dane Bell | 02 August 2016, 21:40:32 UTC | Tests for issue 259 | 02 August 2016, 21:40:32 UTC |
| bf5e27b | Gus Hahn-Powell | 02 August 2016, 21:13:01 UTC | Merge pull request #302 from clulab/issue150 Prevent BioProcesses from being controllers (except of other BioProcesses) | 02 August 2016, 21:13:01 UTC |
| 7e9c290 | Marco Antonio Valenzuela Escárcega | 02 August 2016, 20:06:00 UTC | Turn n-ary complex into n-ary binding event | 02 August 2016, 20:06:00 UTC |
| 444ab9e | Dane Bell | 02 August 2016, 19:10:29 UTC | Filter out bioprocess-controlled complex events | 02 August 2016, 19:10:29 UTC |
| 2670c28 | Dane Bell | 02 August 2016, 19:03:49 UTC | Add tests for issue150 | 02 August 2016, 19:03:49 UTC |
| 1b19f86 | Gus Hahn-Powell | 02 August 2016, 11:14:13 UTC | Only unigrams and bigrams | 02 August 2016, 11:14:13 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 |
