| 79c9094 | Denis Yuen | 02 August 2016, 15:43:15 UTC | [maven-release-plugin] prepare release 0.4-beta.5 | 02 August 2016, 15:43:15 UTC |
| ddba429 | Denis Yuen | 02 August 2016, 15:39:34 UTC | Iterate version numbers | 02 August 2016, 15:39:34 UTC |
| c0f129d | Denis Yuen | 02 August 2016, 15:30:50 UTC | [maven-release-plugin] prepare release 0.4-beta.4 | 02 August 2016, 15:30:50 UTC |
| 728c77c | Denis Yuen | 02 August 2016, 15:09:42 UTC | Feature/more tool registry changes (#358) * jacoco is redundant, coveralls hooked up to cobertura * Add offset and limit parameters * Implement naive pagination Needs a more efficient implementation when Dockstore gets big * Fix findbugs, code still ugly though | 02 August 2016, 15:09:42 UTC |
| 6aa8f34 | Denis Yuen | 29 July 2016, 16:55:57 UTC | Make sure we return a 404 when format is incorrect (#353) | 29 July 2016, 16:55:57 UTC |
| 19c7488 | Denis Yuen | 28 July 2016, 21:27:22 UTC | Feature/coverity cleanup (#351) * Update to dropwizard 1.0 * a bit of cleanup * Update GA4GH endpoints for tool-registry-schema to the proposed 1.0.0 | 28 July 2016, 21:27:22 UTC |
| 12fb6ff | Denis Yuen | 26 July 2016, 21:06:57 UTC | Update README.md | 26 July 2016, 21:06:57 UTC |
| af94150 | Denis Yuen | 26 July 2016, 20:35:36 UTC | Update README.md | 26 July 2016, 20:35:36 UTC |
| 77d4513 | Denis Yuen | 21 July 2016, 19:42:06 UTC | Feature/dockstore classpath (#342) * Fix classpath for server * Update PULL_REQUEST_TEMPLATE.md | 21 July 2016, 19:42:06 UTC |
| 1eddb5f | Denis Yuen | 20 July 2016, 18:24:07 UTC | Update ISSUE_TEMPLATE.md | 20 July 2016, 18:24:07 UTC |
| 6e945b1 | Denis Yuen | 20 July 2016, 18:19:55 UTC | Fix typo | 20 July 2016, 18:19:55 UTC |
| 5122e84 | Denis Yuen | 20 July 2016, 18:14:57 UTC | Feature/docs (#340) * Separate users and developers * Create CONTRIBUTING.md * Create ISSUE_TEMPLATE.md * Create PULL_REQUEST_TEMPLATE.md * Add documents to help contributors and users | 20 July 2016, 18:14:57 UTC |
| 95a7fe7 | Denis Yuen | 19 July 2016, 17:49:57 UTC | Update to CWL v1.0 (#334) * Update to CWL v1.0 * mostly updates to the launcher and the test workflow/tool * Update build versions of cwltool to work with v1.0 * Re-organise provisioning * Looks like cwltool's dependencies have changed Conflicts: .travis.yml * Deprecated * Finish wrestling with slf4j * Fix for #339, missing cast for double (weird) * Update readme.md | 19 July 2016, 17:49:57 UTC |
| 6057432 | Denis Yuen | 18 July 2016, 20:13:47 UTC | Feature/security updates (#338) * Properly set scope for mocking dependencies and update security issues * Looks like cwltool's dependencies have changed | 18 July 2016, 20:13:47 UTC |
| 9f9117c | Janice Patricia | 14 July 2016, 19:57:02 UTC | Feature/dockstore 328 streamline tool path (#333) * added webservice resource to update tool paths on tags * changed return type method * added test for cwl wdl and dockerfile path * get rid of refresh after set default on test | 14 July 2016, 19:57:02 UTC |
| fc30e41 | Janice Patricia | 13 July 2016, 15:43:38 UTC | Feature/dockstore 284 streamline path descriptor (#327) * update workflow path of versions * try not pulling nodejs engine * separate update into a new method * added test and helper | 13 July 2016, 15:43:38 UTC |
| c53f3f3 | Brian O'Connor | 09 July 2016, 16:28:39 UTC | Update README.md | 09 July 2016, 16:28:39 UTC |
| a26dbf7 | Denis Yuen | 08 July 2016, 19:24:32 UTC | gitter | 08 July 2016, 19:24:32 UTC |
| 69f215f | Denis Yuen | 08 July 2016, 18:46:05 UTC | Give this a shot (#326) | 08 July 2016, 18:46:05 UTC |
| 4066c9f | Janice Patricia | 07 July 2016, 19:06:52 UTC | Fix validation check (#321) * add baseCommand warning & remove ':' syntax check * put back ':' check | 07 July 2016, 19:06:52 UTC |
| a81c324 | Janice Patricia | 07 July 2016, 14:25:53 UTC | Feature/dockstore 296 tool tab (#315) * base code for generating tool json string will still need to give comments or javadocs for each methods will need to double check on the data structure will need to test more and create a testIT for this feature * added comments and merged dag code class is always DockerRequirement, so no need to show it show "Not Specified" instead of blank * fix and refactor code unchanged: tempDescriptor file, because it's needed for WDL as in WDL it will be passed as a File to scala | 07 July 2016, 14:25:53 UTC |
| 8c3d584 | Denis Yuen | 07 July 2016, 13:56:38 UTC | Feature/resources for specific version (#320) * Add migration #303 * Attempt to sort yaml * Tackle #228, make sure ordering of swagger.yaml does not randomly change * Activate some disabled tests and test caching | 07 July 2016, 13:56:38 UTC |
| 8851199 | Denis Yuen | 06 July 2016, 17:29:07 UTC | Properly expose and report YAML parser errors to the GUI (#318) | 06 July 2016, 17:29:07 UTC |
| 4aadbcd | Denis Yuen | 06 July 2016, 17:16:09 UTC | Update README.md | 06 July 2016, 17:16:09 UTC |
| 7340f60 | Denis Yuen | 06 July 2016, 17:15:08 UTC | Update README.md | 06 July 2016, 17:15:08 UTC |
| 654769c | Denis Yuen | 06 July 2016, 14:40:04 UTC | Update GA4GH and broaden endpoints (#314) * Update GA4GH and broaden endpoints * response type overrides type in path * Add a couple of tests | 06 July 2016, 14:40:04 UTC |
| 4fd837e | Denis Yuen | 04 July 2016, 16:37:52 UTC | Upgrade to google-oauth-java-client (#312) | 04 July 2016, 16:37:52 UTC |
| 89f7be0 | Janice Patricia | 04 July 2016, 16:09:52 UTC | Dag run syntax fix 306 (#309) * run import bracket syntax fixed * refactor code * another test added for syntax | 04 July 2016, 16:09:52 UTC |
| 8e8ad23 | Janice Patricia | 28 June 2016, 14:35:56 UTC | DAG workflow integration test (#305) | 28 June 2016, 14:35:56 UTC |
| 42c8b7c | Denis Yuen | 24 June 2016, 19:40:32 UTC | Squash error when release version does not exist (#302) * i.e. when testing a new release version | 24 June 2016, 19:40:32 UTC |
| 9c5d7b5 | Denis Yuen | 24 June 2016, 17:32:41 UTC | [maven-release-plugin] prepare for next development iteration | 24 June 2016, 17:32:41 UTC |
| 653690f | Denis Yuen | 24 June 2016, 17:32:39 UTC | [maven-release-plugin] prepare release 0.4-beta.3 | 24 June 2016, 17:32:39 UTC |
| 910c627 | Janice Patricia | 24 June 2016, 14:28:14 UTC | Feature/workflow dag resource (#298) * Initial DAG resource * More changes to DAG * Added support for CWLtools having different docker envs, also some comment * cwl dag bug fixed * wdl dag now working * if no dockerfile, the tool node will not open anything * if there is dockerfile, the tool node will open a new tab opening the docker link * need to hide 'Tool' tab and create a new issue for that | 24 June 2016, 14:28:14 UTC |
| 6e31e56 | Denis Yuen | 24 June 2016, 13:30:32 UTC | Feature/cobertura experiment (#297) * Properly ignore trivial and generated code * Hook up VersionEye * Weird, why did this change? * Set version eye project id * Do not create extra properties file * Meh * vfs 2.1 seems to have issues | 24 June 2016, 13:30:32 UTC |
| 3886134 | Denis Yuen | 22 June 2016, 20:07:22 UTC | Fix refresh behaviour and add test (#295) * Fix refresh behaviour and add test * Support yaml and yml extensions for CWL #289 * Fix formatting for client #291 | 22 June 2016, 20:07:22 UTC |
| e2aba52 | Denis Yuen | 20 June 2016, 15:55:40 UTC | [maven-release-plugin] prepare for next development iteration | 20 June 2016, 15:55:40 UTC |
| e54b781 | Denis Yuen | 20 June 2016, 15:55:38 UTC | [maven-release-plugin] prepare release 0.4-beta.2 | 20 June 2016, 15:55:38 UTC |
| 67caef8 | Denis Yuen | 16 June 2016, 19:09:37 UTC | Add feature to turn on and off caching (#281) | 16 June 2016, 19:09:37 UTC |
| a45760a | Denis Yuen | 16 June 2016, 19:07:30 UTC | Feature/dead code cleanup (#282) * Clean up some dead code and expand tests * Just some annoyances | 16 June 2016, 19:07:30 UTC |
| 3cd0dfe | Denis Yuen | 16 June 2016, 17:14:06 UTC | Feature/dockstore api cleanup (#279) * Clarify message when quay.io token is not available * Working on #263 and #262 Implemented imports for CWL tools and handled some error cases for GA4GH endpoints * Tackle #208 and #263 * Re-use import code between workflows and tools * Support include as well as import, also bare "run" in workflows * Work on #263, #208, #267 * Expand error conditions * Re-use import code for workflows and tools * Migrate some code to use source code factory * Fix for various tests, mostly Bitbucket | 16 June 2016, 17:14:06 UTC |
| 3c260fb | Brian O'Connor | 15 June 2016, 14:30:05 UTC | passing in tmpdir to cwltool command (#277) | 15 June 2016, 14:30:05 UTC |
| 7f9062f | Janice Patricia | 10 June 2016, 17:07:25 UTC | Feature/dockstore 260 entry file launch validation (#261) * fixed cwl file validation * fixed checking cwl file * added cwl file for testing * added baseCommand check and warning * LaunchTestIT can now test cwl launch * ignored back all cwl launch tests * added cwlVersion check on the file * fixed wdl file validation * fixed if position for travis * Delete Dockstore.cwl * Delete Dockstore.json * added tests on warnings and errors * restructure warning * fixed cwl tool and workflow validation check workflow and tool cwl file validation fixed comments added fixed output message for LaunchTestIT * added documentation and comments | 10 June 2016, 17:07:25 UTC |
| 4b3b6a6 | Denis Yuen | 10 June 2016, 15:12:29 UTC | Feature/dockstore 263 fix tests (#265) * Update tests to add constraint * Also clean up DB loading code * update secret archive * Test out updated database * Fix path (travis utility gives incorrect path) * Update postgres version | 10 June 2016, 15:12:29 UTC |
| dbad216 | Denis Yuen | 08 June 2016, 20:26:40 UTC | Feature/virtual directory experiment (#264) * Implement endpoints to hit up secondary files * Fix non-deterministic test * Do testing for workflows Next stop, tools * Fix again, test data invalid * Add more GA4GH test * Lame test to touch on all help messages * Fix environment * A bit more locking down of CLI operations | 08 June 2016, 20:26:40 UTC |
| 5f154b3 | Denis Yuen | 03 June 2016, 19:43:49 UTC | Update README.md | 03 June 2016, 19:43:49 UTC |
| 8e93d10 | Denis Yuen | 03 June 2016, 19:43:06 UTC | Feature/jacoco experiment (#257) * Delete migrated doc * Match Dropwizard's own config and try aggregate with cobertura * Cache .m2 directory * Oddly, separating the report goal from generation avoids a hang on Travis-CI, no idea why | 03 June 2016, 19:43:06 UTC |
| 99ffe0d | Denis Yuen | 01 June 2016, 20:14:30 UTC | Clean up build logging (#254) | 01 June 2016, 20:14:30 UTC |
| e5945e2 | Denis Yuen | 31 May 2016, 20:10:09 UTC | tackle #251 , invalid tokens should result in a warning and quick abort (#252) * tackle #251 , invalid tokens should result in a warning and quick abort * Return null for missing files though | 31 May 2016, 20:10:09 UTC |
| 800370c | Janice Patricia | 26 May 2016, 18:55:10 UTC | Merge branch 'develop' of github.com:ga4gh/dockstore into develop | 26 May 2016, 18:55:10 UTC |
| fa55285 | Janice Patricia | 26 May 2016, 18:54:55 UTC | Add comments to example yaml file | 26 May 2016, 18:54:55 UTC |
| a663219 | Denis Yuen | 26 May 2016, 17:31:50 UTC | Feature/test out jacoco (#247) * Hook up jacoco * Hook up coveralls.io * Clean up some stuff left in working directory during build | 26 May 2016, 17:31:50 UTC |
| 7205883 | Janice Patricia | 25 May 2016, 21:00:18 UTC | Feature/dockstore 223 cli launch simplification (#243) * Add file for testing * cli launch simplification * moved else if stmt * a bit of refactoring * changed FileReader to InputStreamReader * got rid of error msg in MocketIT.java * separate local entry and entry * moved else statements * changed '' into null * add test file * refactor code and test * changed system exit back into errormsg * add config file * refactor code and LaunchTestIT * setConfigFile from private to public * fixed code checkCWL method | 25 May 2016, 21:00:18 UTC |
| 29d0cde | Denis Yuen | 25 May 2016, 16:53:11 UTC | Feature/cwl file provisioning (#246) * Is #195 still a thing? * Display cwltool commands #241 * As is, UpgradeTestIT seems to be testing a test method? Disabling for now * Fix #242, tutorial CWL workflow does not use a # identifier * Implement Synapse in file provisioning #244 New config keys in ~/.dockstore/config * synapse-api-key * synapse-user-name | 25 May 2016, 16:53:11 UTC |
| 7331f70 | Denis Yuen | 19 May 2016, 00:37:51 UTC | Feature/dockstore 128 basic caching (#239) * Clean up paths * Implement basic caching Uses git-like structure * configure directory using `cache-dir` value in config file * takes advantage of hardlinking to maintain copies of cached data * Clean cache and duplicate removal * Create cache on Travis | 19 May 2016, 00:37:51 UTC |
| ff79806 | Janice Patricia | 18 May 2016, 20:01:48 UTC | refactor code and changed upgradeTestIT (#238) * refactor code and changed upgradeTestIT * moved 'decideOutput' method to 'UpgradeTestIT' * deleted json files that are not needed anymore | 18 May 2016, 20:01:48 UTC |
| a2833ea | Denis Yuen | 18 May 2016, 17:17:00 UTC | Feature/wdl output provisioning (#237) * Bring up WDL launching output up to CWL standard * Implement file provisoning for WDL Needs testing in second pull request | 18 May 2016, 17:17:00 UTC |
| 7e0c81d | Denis Yuen | 17 May 2016, 18:04:45 UTC | Iterate to next development version | 17 May 2016, 18:04:45 UTC |
| 8605ac7 | Denis Yuen | 17 May 2016, 17:59:56 UTC | Merge tag '0.4-beta.1' into develop [maven-release-plugin] copy for tag 0.4-beta.1 | 17 May 2016, 17:59:56 UTC |
| 72e122c | Denis Yuen | 16 May 2016, 20:38:44 UTC | [maven-release-plugin] prepare release 0.4-beta.1 | 16 May 2016, 20:38:44 UTC |
| 149de35 | Denis Yuen | 16 May 2016, 20:33:29 UTC | Tests break release of new versions | 16 May 2016, 20:33:29 UTC |
| 4b9f9ea | Denis Yuen | 16 May 2016, 20:17:21 UTC | Revert "Iterate version numbers" This reverts commit 0523f2a25882ea6d905692e00279f268262a8e56. | 16 May 2016, 20:17:21 UTC |
| 5899b8a | Denis Yuen | 16 May 2016, 20:12:47 UTC | Odd hotfix issue, refreshed tools unpublish themselves | 16 May 2016, 20:12:47 UTC |
| 0523f2a | Denis Yuen | 16 May 2016, 20:12:29 UTC | Iterate version numbers | 16 May 2016, 20:12:29 UTC |
| e781989 | Denis Yuen | 16 May 2016, 16:05:17 UTC | Expand readme.md #233 (#234) | 16 May 2016, 16:05:17 UTC |
| 3e18355 | Brian O'Connor | 13 May 2016, 22:30:05 UTC | update | 13 May 2016, 22:30:05 UTC |
| 43e98ff | Brian O'Connor | 13 May 2016, 22:28:56 UTC | update | 13 May 2016, 22:28:56 UTC |
| 63f9d22 | Brian O'Connor | 13 May 2016, 22:27:41 UTC | changes to functional spec | 13 May 2016, 22:27:41 UTC |
| 9b62ec8 | Brian O'Connor | 13 May 2016, 22:12:34 UTC | starting a document to help align Shizhou's work | 13 May 2016, 22:12:34 UTC |
| 9acdfe3 | Janice Patricia | 13 May 2016, 17:21:17 UTC | Feature/dockstore 196 intuitive upgrading (#227) Added options to upgrade/downgrade to stable/unstable version of dockstore Also, added UpgradeIT and refactored tests | 13 May 2016, 17:21:17 UTC |
| 2df21db | Denis Yuen | 12 May 2016, 15:29:45 UTC | Feature/dockstore launcher output (#231) * Take control of logging * Add progress indicator * Expand debug mode and make launcher output more friendly * Fix formatting issue * Squelch annoying output | 12 May 2016, 15:29:45 UTC |
| 6eb1c18 | Denis Yuen | 10 May 2016, 20:57:49 UTC | Feature/dockstore 197 reorg options (#229) * Focus the usage message * Get rid of a few instances of code duplicates | 10 May 2016, 20:57:49 UTC |
| 3e17c02 | Denis Yuen | 10 May 2016, 20:57:43 UTC | Make refresh log separated by user (#230) | 10 May 2016, 20:57:43 UTC |
| 5c18672 | Denis Yuen | 10 May 2016, 18:54:50 UTC | Fix tests for #192 (#225) * Fix tests for #192 * Re-enable tests * Fix mocking | 10 May 2016, 18:54:50 UTC |
| 3123e31 | Denis Yuen | 29 April 2016, 21:14:29 UTC | Update README.md | 29 April 2016, 21:14:29 UTC |
| 99b6d98 | Andrew Duncan | 29 April 2016, 20:39:05 UTC | [maven-release-plugin] prepare for next development iteration | 29 April 2016, 20:39:05 UTC |
| da87319 | Andrew Duncan | 29 April 2016, 20:39:00 UTC | [maven-release-plugin] prepare release 0.4-beta.0 | 29 April 2016, 20:39:00 UTC |
| e194817 | Denis Yuen | 29 April 2016, 18:43:55 UTC | Merge pull request #207 from ga4gh/feature/tag_refresh_issue Only re-create tags when required | 29 April 2016, 18:43:55 UTC |
| ebdfe93 | Andrew Duncan | 29 April 2016, 15:53:34 UTC | Drop useless default value from tool and tag IDs | 29 April 2016, 15:53:34 UTC |
| e5e9c3b | Andrew Duncan | 28 April 2016, 21:15:42 UTC | Initial attempt at getting migration working | 28 April 2016, 21:15:42 UTC |
| 4dd887a | Denis Yuen | 28 April 2016, 17:28:03 UTC | Merge pull request #209 from ga4gh/feature/cwl_workflow_file_provisioning Feature/cwl workflow file provisioning | 28 April 2016, 17:28:03 UTC |
| 63f1fc2 | Denis Yuen | 28 April 2016, 17:14:08 UTC | Remove un-needed version | 28 April 2016, 17:14:08 UTC |
| 847ce01 | Andrew Duncan | 28 April 2016, 16:37:59 UTC | added missing dependency | 28 April 2016, 16:37:59 UTC |
| e2f46be | Denis Yuen | 28 April 2016, 16:19:13 UTC | Merge branch 'feature/cwl_workflow_file_provisioning' of github.com:ga4gh/dockstore into feature/cwl_workflow_file_provisioning | 28 April 2016, 16:19:13 UTC |
| f70f1d9 | Denis Yuen | 28 April 2016, 16:18:57 UTC | Looks like swagger definition has changed at some point | 28 April 2016, 16:18:57 UTC |
| ff58acc | Denis Yuen | 28 April 2016, 16:18:31 UTC | Refactor to remove (well-intentioned) copy-paste | 28 April 2016, 16:18:31 UTC |
| 53ccc20 | Andrew Duncan | 28 April 2016, 16:13:16 UTC | Moved test files to proper location | 28 April 2016, 16:13:16 UTC |
| d3af6c7 | Andrew Duncan | 28 April 2016, 14:23:32 UTC | Merge branch 'develop' into feature/cwl_workflow_file_provisioning | 28 April 2016, 14:23:32 UTC |
| b70086b | Denis Yuen | 27 April 2016, 21:10:30 UTC | Update README.md | 27 April 2016, 21:10:30 UTC |
| 554be79 | Denis Yuen | 27 April 2016, 20:01:02 UTC | Update README.md | 27 April 2016, 20:01:02 UTC |
| 43c28da | Denis Yuen | 27 April 2016, 19:52:20 UTC | Update README.md | 27 April 2016, 19:52:20 UTC |
| c995cc0 | Andrew Duncan | 27 April 2016, 19:38:58 UTC | Reorganized file provisioning code | 27 April 2016, 19:38:58 UTC |
| 1c1c550 | Andrew Duncan | 27 April 2016, 19:23:05 UTC | Initial attempt at cwl workflow file provisioning | 27 April 2016, 19:23:05 UTC |
| 748b8a7 | Denis Yuen | 27 April 2016, 18:41:41 UTC | Fix formatting issue | 27 April 2016, 18:41:41 UTC |
| 82c59fc | Denis Yuen | 27 April 2016, 18:25:43 UTC | Only re-create tags when required | 27 April 2016, 18:25:43 UTC |
| b812795 | Andrew Duncan | 22 April 2016, 17:31:22 UTC | [maven-release-plugin] prepare for next development iteration | 22 April 2016, 17:31:22 UTC |
| fac69f2 | Andrew Duncan | 22 April 2016, 17:31:20 UTC | [maven-release-plugin] prepare release 0.4-alpha.1 | 22 April 2016, 17:31:20 UTC |
| 26f2de1 | Andrew Duncan | 22 April 2016, 17:26:45 UTC | Fix for db migration | 22 April 2016, 17:26:45 UTC |
| 9413a82 | Andrew Duncan | 22 April 2016, 16:21:23 UTC | [maven-release-plugin] prepare for next development iteration | 22 April 2016, 16:21:23 UTC |
| 0cd4ab0 | Andrew Duncan | 22 April 2016, 16:16:17 UTC | [maven-release-plugin] prepare release 0.4-alpha.0 | 22 April 2016, 16:16:17 UTC |
| f2dfe88 | Andrew Duncan | 22 April 2016, 16:06:39 UTC | [maven-release-plugin] rollback the release of 0.4-alpha.0 | 22 April 2016, 16:06:39 UTC |
