| 150da5e | Keith Alcock | 28 February 2024, 23:32:34 UTC | Merge pull request #805 from clulab/kwalcock/badge Update badge protocol | 28 February 2024, 23:32:34 UTC |
| a2d2629 | Keith Alcock | 28 February 2024, 20:08:34 UTC | Update badge protocol | 28 February 2024, 20:08:34 UTC |
| 2582b16 | Enrique Noriega | 09 February 2024, 19:47:09 UTC | Merge pull request #804 from clulab/resource_update Update key named entity resource files to latest state | 09 February 2024, 19:47:09 UTC |
| b2d88f2 | Ben Gyori | 09 February 2024, 16:55:24 UTC | Fix the type of event we look for in the test | 09 February 2024, 16:55:24 UTC |
| 7f31bda | Ben Gyori | 08 February 2024, 21:40:06 UTC | Update test to reflect improved output | 08 February 2024, 21:40:23 UTC |
| 1fac177 | Ben Gyori | 08 February 2024, 21:10:16 UTC | Reinstate COVID-19 override curations | 08 February 2024, 21:10:16 UTC |
| c00d1f2 | Ben Gyori | 08 February 2024, 20:52:31 UTC | Improve FamPlex terms and overrides | 08 February 2024, 20:52:31 UTC |
| be50477 | Ben Gyori | 08 February 2024, 20:25:03 UTC | Update test to reflect new GO term recognized | 08 February 2024, 20:25:23 UTC |
| 27d4a28 | Ben Gyori | 08 February 2024, 14:49:45 UTC | Add script for uniprot subcell and update | 08 February 2024, 14:49:45 UTC |
| a5659e7 | Ben Gyori | 08 February 2024, 14:14:03 UTC | Update UniProt resource files | 08 February 2024, 14:14:03 UTC |
| 852ce9c | Ben Gyori | 08 February 2024, 14:13:48 UTC | Remove deprecated code to get additional SARS-CoV-2 synonyms | 08 February 2024, 14:13:48 UTC |
| db24283 | Ben Gyori | 08 February 2024, 14:13:03 UTC | Update UniProt download to new API | 08 February 2024, 14:13:03 UTC |
| f33b432 | Ben Gyori | 24 January 2024, 02:42:18 UTC | Update protein ontology | 24 January 2024, 02:42:18 UTC |
| 1426ec3 | Ben Gyori | 24 January 2024, 02:38:46 UTC | Update GO | 24 January 2024, 02:38:46 UTC |
| 3e62fcb | Ben Gyori | 24 January 2024, 02:08:08 UTC | Update FamPlex entries and override | 24 January 2024, 02:08:08 UTC |
| 065f274 | Ben Gyori | 23 January 2024, 21:32:58 UTC | Update ChEBI and MeSH | 23 January 2024, 21:32:58 UTC |
| 122dbaa | Enrique Noriega | 20 October 2023, 21:34:47 UTC | Merge pull request #803 from clulab/bioresources_build Add bioresources to build | 20 October 2023, 21:34:47 UTC |
| 4790865 | Ben Gyori | 18 October 2023, 02:06:11 UTC | Add bioresources to build | 18 October 2023, 02:06:11 UTC |
| 168b58f | Keith Alcock | 30 June 2023, 14:22:24 UTC | Merge pull request #798 from clulab/kwalcock/sbtassembly Update assembly conflict resolution | 30 June 2023, 14:22:24 UTC |
| b1f75d2 | Keith Alcock | 28 June 2023, 20:11:56 UTC | Update assembly conflict resolution | 28 June 2023, 20:11:56 UTC |
| c7397a4 | Keith Alcock | 17 January 2023, 00:16:03 UTC | Merge pull request #780 from clulab/kwalcock/processorsUpdate Update processors | 17 January 2023, 00:16:03 UTC |
| d1cfd9a | Keith Alcock | 16 January 2023, 20:58:22 UTC | Fix build badge | 16 January 2023, 20:58:22 UTC |
| bb711b7 | Keith Alcock | 16 January 2023, 20:34:18 UTC | Update processors | 16 January 2023, 20:34:18 UTC |
| 3dbf61b | Keith Alcock | 16 January 2023, 20:31:26 UTC | Ignore more files | 16 January 2023, 20:31:26 UTC |
| ad4ce51 | Keith Alcock | 16 January 2023, 20:31:07 UTC | Fix compilation | 16 January 2023, 20:31:07 UTC |
| 41245f7 | Keith Alcock | 09 January 2023, 15:10:22 UTC | Merge pull request #778 from clulab/kwalcock/clulab Change to clulab dependency | 09 January 2023, 15:10:22 UTC |
| ea7602f | Keith Alcock | 08 January 2023, 01:36:58 UTC | Revert that sh thing | 08 January 2023, 01:36:58 UTC |
| 45f476e | Keith Alcock | 08 January 2023, 01:29:18 UTC | Increase a timeout Start sbt directly rather than through sh | 08 January 2023, 01:29:18 UTC |
| 74a2679 | Keith Alcock | 07 January 2023, 20:35:48 UTC | Add even more If this doesn't work, I'll make sure that tests aren't running in parallel. | 07 January 2023, 20:35:48 UTC |
| 2a5bc0a | Keith Alcock | 07 January 2023, 05:35:20 UTC | Use more memory | 07 January 2023, 05:35:20 UTC |
| 6cc52e3 | Keith Alcock | 07 January 2023, 00:30:32 UTC | Allow more memory for testing | 07 January 2023, 00:30:32 UTC |
| 1bf4d70 | Keith Alcock | 06 January 2023, 21:34:34 UTC | Convert from Java to Scala explicitly | 06 January 2023, 21:34:34 UTC |
| 935a9c6 | Keith Alcock | 06 January 2023, 17:29:01 UTC | Run multiple tests via aggregation This does mean that the processors subproject is aggregated into compilation, which is a change in behavior. I don't think that will hurt. | 06 January 2023, 17:29:01 UTC |
| 4071008 | Keith Alcock | 05 January 2023, 22:41:57 UTC | Change to clulab dependency | 05 January 2023, 22:41:57 UTC |
| add4859 | Enrique Noriega | 18 November 2022, 22:15:12 UTC | Merge pull request #775 from clulab/section_names Added support to extract section names | 18 November 2022, 22:15:12 UTC |
| bc72ac3 | Enrique Noriega | 18 November 2022, 01:48:53 UTC | Update ReachCLI.scala | 18 November 2022, 01:48:53 UTC |
| a8c6b32 | Enrique Noriega | 18 November 2022, 01:47:08 UTC | Update FriesOutput.scala | 18 November 2022, 01:47:08 UTC |
| 0df2b30 | Enrique Noriega | 18 November 2022, 00:36:32 UTC | Use the implicit converter to make things nicer | 18 November 2022, 00:36:32 UTC |
| ffed65a | Enrique Noriega | 17 November 2022, 23:47:27 UTC | Merge pull request #776 from clulab/kwalcock/section_names2 This is one way to add section names without changes to processors | 17 November 2022, 23:47:27 UTC |
| fca5973 | Enrique Noriega | 17 November 2022, 22:53:54 UTC | Some fixes to carry these changes forward to FriesOutput | 17 November 2022, 22:53:54 UTC |
| e678cbe | Keith Alcock | 16 November 2022, 16:21:44 UTC | Account for sections on plain Documents | 16 November 2022, 16:22:12 UTC |
| a6e3840 | Keith Alcock | 16 November 2022, 15:36:06 UTC | Allow for reading of standard document format | 16 November 2022, 15:36:06 UTC |
| 55b7c89 | Keith Alcock | 16 November 2022, 01:50:01 UTC | Change to inheritance for document serialization | 16 November 2022, 01:50:01 UTC |
| af7fd68 | Keith Alcock | 16 November 2022, 01:38:35 UTC | Add document serialization and testing | 16 November 2022, 01:38:35 UTC |
| d43be70 | Keith Alcock | 15 November 2022, 23:23:52 UTC | Unsnapshot processors | 15 November 2022, 23:23:52 UTC |
| 10e3c69 | Keith Alcock | 15 November 2022, 23:13:12 UTC | Begin serialization | 15 November 2022, 23:13:12 UTC |
| 4dcf28d | Keith Alcock | 15 November 2022, 22:30:49 UTC | Option 2 Rather than pass around a ReachDocument, just convert Sentences that need to know about sections to ReachSentences. | 15 November 2022, 22:30:49 UTC |
| 24eb778 | Enrique Noriega | 14 November 2022, 19:22:26 UTC | Merge remote-tracking branch 'origin/section_names' into section_names | 14 November 2022, 19:22:26 UTC |
| b955e5b | Enrique Noriega | 14 November 2022, 17:19:54 UTC | Added support to look at xml files. PubMed recently stopped using the nxml extension in favor of xml | 14 November 2022, 19:02:38 UTC |
| 09e4f97 | Enrique Noriega | 14 November 2022, 17:19:54 UTC | Added support to look at xml files. PubMed recently stopped using the nxml extension in favor of xml | 14 November 2022, 17:19:54 UTC |
| 020ab29 | Enrique Noriega | 13 November 2022, 23:10:16 UTC | Merged master into the branch before PR | 13 November 2022, 23:10:16 UTC |
| 8b36655 | Enrique Noriega | 13 November 2022, 23:03:24 UTC | Merge remote-tracking branch 'origin/master' into section_names # Conflicts: # main/src/main/scala/org/clulab/reach/ReachSystem.scala # src/main/scala/org/clulab/reach/AnnotationsCLI.scala # src/main/scala/org/clulab/reach/ReachCLI.scala | 13 November 2022, 23:03:24 UTC |
| 24f0ad5 | Enrique Noriega | 13 November 2022, 17:36:49 UTC | Added section names to FriesOutput | 13 November 2022, 17:36:49 UTC |
| baa6b5a | Enrique Noriega | 13 November 2022, 17:21:50 UTC | Added support for serialization of section names | 13 November 2022, 17:21:50 UTC |
| 2dbf7da | Enrique Noriega | 09 June 2022, 22:38:42 UTC | Merge pull request #769 from clulab/serialization Improved ahead-of-time annotator `AnnotationsCLI` | 09 June 2022, 22:38:42 UTC |
| 1a4b516 | Enrique Noriega | 09 June 2022, 19:58:45 UTC | Fixed `TestBioNLPProcessor` | 09 June 2022, 19:58:45 UTC |
| 0d36940 | Enrique Noriega | 09 June 2022, 02:06:43 UTC | Trigger a build | 09 June 2022, 02:06:43 UTC |
| addea59 | Enrique Noriega | 08 June 2022, 20:21:12 UTC | Fixed a bug in which rule-based NER wasn't happening if calling directly `extractEntities` | 08 June 2022, 20:21:12 UTC |
| fcbd398 | Enrique Noriega | 08 June 2022, 19:27:15 UTC | Merge branch 'master' into serialization | 08 June 2022, 19:27:15 UTC |
| a31d349 | Enrique Noriega | 02 May 2022, 23:16:28 UTC | Construct section names and add them to Sentence instances when annotating papers | 02 May 2022, 23:16:28 UTC |
| 1cc9184 | Enrique Noriega | 22 April 2022, 22:32:56 UTC | Added the section name intervals to FriesEntry | 22 April 2022, 22:32:56 UTC |
| 7f5648b | Enrique Noriega | 22 April 2022, 20:36:56 UTC | Progress on addding section titles | 22 April 2022, 20:36:56 UTC |
| d42aaf6 | Benjamin M. Gyori | 10 April 2022, 22:45:23 UTC | Change to runMain (#770) | 10 April 2022, 22:45:23 UTC |
| b7b6868 | Enrique Noriega | 29 March 2022, 17:28:40 UTC | Removed unnecessary method from `FriesEntry` | 29 March 2022, 17:28:40 UTC |
| ce63ad4 | Enrique Noriega | 28 March 2022, 23:25:41 UTC | Decoupled rule and crf NER steps in ReachSystem | 28 March 2022, 23:25:41 UTC |
| 986119e | Enrique Noriega | 28 March 2022, 20:33:13 UTC | Replaced the normal serializer with `DocumentSerializer` | 28 March 2022, 20:33:13 UTC |
| 28c1414 | Enrique Noriega | 25 March 2022, 03:28:54 UTC | Merge pull request #768 from clulab/bioresources_docs | 25 March 2022, 03:28:54 UTC |
| 4574f21 | Enrique Noriega | 21 March 2022, 18:25:17 UTC | Fixed the tests to pull the KB file names directly from `application.conf` in the bioresources subdir | 21 March 2022, 18:25:17 UTC |
| 8c6da62 | Ben Gyori | 21 March 2022, 13:57:25 UTC | Reinstate some constants | 21 March 2022, 13:57:25 UTC |
| 6935a26 | Ben Gyori | 21 March 2022, 13:35:55 UTC | Remove unused path constants | 21 March 2022, 13:35:55 UTC |
| 5e0be03 | Ben Gyori | 21 March 2022, 13:33:13 UTC | Remove deprecated NER files from version control | 21 March 2022, 13:33:13 UTC |
| b575a08 | Ben Gyori | 21 March 2022, 13:32:47 UTC | Remove deprecated NER config file | 21 March 2022, 13:32:47 UTC |
| 7115d90 | Ben Gyori | 21 March 2022, 13:32:34 UTC | Update Bioresources docs | 21 March 2022, 13:32:34 UTC |
| befec11 | Keith Alcock | 24 February 2022, 19:46:32 UTC | Add citations (#767) * Add citations * Add diacritic * Try preferred-citation * Make sure it can be parsed * Use preferred-citation * Replace missing { * Try publisher differently * Revert "Try publisher differently" This reverts commit 04210c73b4a2ddd8a34fa7aa6ad271ee0c884514. * Do Marco inconsistently * Add commentary along with preferred citation * Add missing quotation mark | 24 February 2022, 19:46:32 UTC |
| cf7e79f | Keith Alcock | 06 January 2022, 14:52:30 UTC | Merge pull request #763 from clulab/updated_indexer Updated Lucene Indexers | 06 January 2022, 14:52:30 UTC |
| e229e09 | Enrique Noriega | 05 January 2022, 02:35:05 UTC | Added a missing case for pattern matching | 05 January 2022, 02:35:05 UTC |
| 8bbf88c | Enrique Noriega | 05 January 2022, 02:20:04 UTC | Added the pubmed abstract indexer | 05 January 2022, 02:20:04 UTC |
| b4308dd | Enrique Noriega | 28 December 2021, 03:11:01 UTC | Fixed a bug | 28 December 2021, 03:11:01 UTC |
| 7ea0064 | Enrique Noriega | 28 December 2021, 03:04:22 UTC | Fixed a bug | 28 December 2021, 03:04:22 UTC |
| f61d67d | Enrique Noriega | 28 December 2021, 02:46:40 UTC | Find the xml files from the index files directly instead of enumerating a directory | 28 December 2021, 02:46:40 UTC |
| 3ddb3cf | Enrique Noriega | 23 December 2021, 18:53:13 UTC | Made directory search recursive | 23 December 2021, 18:53:13 UTC |
| e4febbc | Enrique Noriega | 23 December 2021, 18:17:43 UTC | Removed unused import | 23 December 2021, 18:17:43 UTC |
| 81c7ecd | Enrique Noriega | 23 December 2021, 18:07:41 UTC | Adapted the index to handle multiple map files (as changed by PMC on dec 21) | 23 December 2021, 18:07:41 UTC |
| a7e5ae6 | Keith Alcock | 16 December 2021, 22:06:06 UTC | Merge pull request #762 from clulab/kwalcock/logging Update logging | 16 December 2021, 22:06:06 UTC |
| 361f03f | Keith Alcock | 16 December 2021, 20:24:17 UTC | Update logging | 16 December 2021, 20:24:17 UTC |
| 13528fd | Keith Alcock | 30 August 2021, 18:12:22 UTC | Merge pull request #761 from clulab/docker Update Docker build | 30 August 2021, 18:12:22 UTC |
| 33c050e | Ben Gyori | 29 August 2021, 02:18:05 UTC | Make wget non-verbose | 29 August 2021, 02:18:05 UTC |
| 9b22f5e | Ben Gyori | 29 August 2021, 02:17:06 UTC | Remove deprecated test Dockerfile and update README | 29 August 2021, 02:17:06 UTC |
| 007b9c6 | Ben Gyori | 29 August 2021, 02:15:56 UTC | Update Dockerfile to new Ubuntu | 29 August 2021, 02:15:56 UTC |
| e487176 | Enrique Noriega | 25 August 2021, 02:22:50 UTC | Merge pull request #760 from clulab/kwalcock/benBug | 25 August 2021, 02:22:50 UTC |
| a6ec1db | Keith Alcock | 24 August 2021, 18:51:32 UTC | Read from resources | 24 August 2021, 18:51:32 UTC |
| 4202758 | Keith Alcock | 24 August 2021, 16:16:49 UTC | Add import to work around warning | 24 August 2021, 16:16:49 UTC |
| e55192d | Keith Alcock | 24 August 2021, 16:00:47 UTC | Fix log message string interpolation | 24 August 2021, 16:00:47 UTC |
| 8fd7382 | Keith Alcock | 24 August 2021, 16:00:20 UTC | Change bioresource path | 24 August 2021, 16:00:20 UTC |
| 9ed6fe0 | Enrique Noriega | 29 June 2021, 16:55:34 UTC | Added the context metadata to the fries output (#757) | 29 June 2021, 16:55:34 UTC |
| 0c51b38 | Mihai Surdeanu | 20 June 2021, 06:55:38 UTC | Merge pull request #756 from clulab/kwalcock/threadUtils Remove superfluous .par | 20 June 2021, 06:55:38 UTC |
| 1698885 | Keith Alcock | 20 June 2021, 00:09:55 UTC | Remove superfluous .par | 20 June 2021, 00:09:55 UTC |
| a086c8c | Mihai Surdeanu | 19 June 2021, 20:17:35 UTC | Merge pull request #753 from clulab/kwalcock/updateProcessors2 Use ThreadUtils, now in processors | 19 June 2021, 20:17:35 UTC |
| 4369a99 | Mihai Surdeanu | 19 June 2021, 11:06:25 UTC | Merge pull request #754 from clulab/hms_context Context Engine Improvements | 19 June 2021, 11:06:25 UTC |
| 44c60cc | Mihai Surdeanu | 19 June 2021, 08:58:45 UTC | Merge pull request #755 from clulab/kwalcock/context Streamline Policies.scala | 19 June 2021, 08:58:45 UTC |
