| abb3a8c | Denis Yuen | 17 October 2017, 17:36:50 UTC | [maven-release-plugin] prepare release 1.3.0-beta.2 | 17 October 2017, 17:36:50 UTC |
| 1dd512e | Denis Yuen | 17 October 2017, 17:34:44 UTC | Iterate pom versions | 17 October 2017, 17:34:44 UTC |
| f031605 | Denis Yuen | 17 October 2017, 17:30:35 UTC | [maven-release-plugin] prepare release 1.3.0-beta.1 | 17 October 2017, 17:30:35 UTC |
| b0165e4 | Denis Yuen | 17 October 2017, 14:24:09 UTC | Workaround aws issue with doubled ending slash (#956) * Workaround aws issue with doubled ending slash | 17 October 2017, 14:24:09 UTC |
| 11bd092 | Denis Yuen | 16 October 2017, 15:45:40 UTC | Content check is not robust enough for workflows (#954) | 16 October 2017, 15:45:40 UTC |
| aaad640 | Denis Yuen | 13 October 2017, 15:43:15 UTC | Minor doc fix (#945) | 13 October 2017, 15:43:15 UTC |
| 64c7a65 | Denis Yuen | 12 October 2017, 15:49:35 UTC | Fix categorization of optional methods (#942) | 12 October 2017, 15:49:35 UTC |
| 0fbdaf2 | Denis Yuen | 12 October 2017, 14:09:26 UTC | Clean up build log a bit (#940) | 12 October 2017, 14:09:26 UTC |
| 4da4f02 | Denis Yuen | 10 October 2017, 18:03:04 UTC | Update copyright notices for production release (#937) | 10 October 2017, 18:03:04 UTC |
| 9343f7e | Denis Yuen | 10 October 2017, 14:58:11 UTC | Trivial fix for swagger catgory, #931 (#935) | 10 October 2017, 14:58:11 UTC |
| 7480121 | Gary Luu | 05 October 2017, 21:12:46 UTC | Handle when both --entry and --local-entry are not present (#934) | 05 October 2017, 21:12:46 UTC |
| 4938123 | Gary Luu | 05 October 2017, 14:08:25 UTC | Update swagger.yaml (#930) * Update swagger.yaml to match new web service annotations * Update to swagger 2.2.3 codegen to fix issues Requires fixes to authentication, string bodies, and a few tests. | 05 October 2017, 14:08:25 UTC |
| d9a17c1 | Denis Yuen | 02 October 2017, 18:10:11 UTC | [maven-release-plugin] prepare for next development iteration | 02 October 2017, 18:10:11 UTC |
| 6a77745 | Denis Yuen | 02 October 2017, 18:10:02 UTC | [maven-release-plugin] prepare release 1.3.0-beta.0 | 02 October 2017, 18:10:02 UTC |
| 1537539 | Denis Yuen | 02 October 2017, 13:12:16 UTC | Add experiment for RSS feed to support potential Discourse integration (#923) * Add experiment for RSS feed to support potential Discourse integration | 02 October 2017, 13:12:16 UTC |
| 31cc7f3 | Denis Yuen | 29 September 2017, 20:00:38 UTC | Guard against #878 looks like UI is submitting incorrect versions (#922) * Guard against #878 looks like UI is submitting incorrect versions | 29 September 2017, 20:00:38 UTC |
| 068bbe4 | Gary Luu | 29 September 2017, 15:21:02 UTC | Feature/refresh by org (#914) * Endpoint for container refresh by organization * Endpoint for refresh workflow by organization * Return no content instead of OK for delete token * Returning all the current tools * Remove unused function * Add auth to endpoints * Change the description of endpoint * Test for endpoint | 29 September 2017, 15:21:02 UTC |
| fe270fb | Gary Luu | 28 September 2017, 15:27:14 UTC | Feature/refresh all indexing (#907) * Moved bulk insert to elastic manager * Bulk index update for tools/workflows that are published * Fix for checkstyle * Don't throw exception when elastic search fails | 28 September 2017, 15:27:14 UTC |
| 2632113 | Denis Yuen | 28 September 2017, 14:06:23 UTC | implement fix for #816 and add test for it (#921) * implement fix for #816 and add test for it * Fix revealed bug with workflow version copying | 28 September 2017, 14:06:23 UTC |
| 37f7f46 | Denis Yuen | 26 September 2017, 18:23:10 UTC | [maven-release-plugin] prepare for next development iteration | 26 September 2017, 18:23:10 UTC |
| ace3797 | Denis Yuen | 26 September 2017, 18:23:06 UTC | [maven-release-plugin] prepare release 1.3.0-alpha.3 | 26 September 2017, 18:23:06 UTC |
| f0eac27 | Denis Yuen | 26 September 2017, 18:02:43 UTC | Update cwltool version for testing (#902) * Update cwltool version for testing | 26 September 2017, 18:02:43 UTC |
| 78fe504 | Denis Yuen | 26 September 2017, 14:53:57 UTC | Feature/cromwell update (#917) * Update cromwell * Functions to launch WDL md5sum, BWA seems problematic, but was problematic with 1.2.5 as well | 26 September 2017, 14:53:57 UTC |
| f2541f4 | Denis Yuen | 26 September 2017, 14:29:24 UTC | Feature/tag cloud (#912) * commit changes to search required to support the tag cloud and auto-complete | 26 September 2017, 14:29:24 UTC |
| f23dd75 | Gary Luu | 25 September 2017, 18:55:54 UTC | Feature/swagger ui update (#909) * Update swagger-ui to 3.1.5 * Added security definition * Sample endpoint that needs authentication, requires Bearer prefix * Add bearer to the swagger ui authentication * Fix for ui2's api calls * Add authentication to endpoints * Add auth to all endpoints * Use contstant for BEARER * fix for checkstyle | 25 September 2017, 18:55:54 UTC |
| 58c7a2a | Gary Luu | 25 September 2017, 13:31:18 UTC | New query for query'ing null workflowname (#908) * New query for query'ing null workflowname * Fix typo | 25 September 2017, 13:31:18 UTC |
| ce828eb | Denis Yuen | 19 September 2017, 15:53:01 UTC | Fix error message and migrate test resource * Transaction needed now * Clean up import * Unwrapped transaction incorrect | 21 September 2017, 21:03:08 UTC |
| c43b73e | Denis Yuen | 19 September 2017, 15:15:54 UTC | Update dropwizard to 1.1.3 | 21 September 2017, 21:03:08 UTC |
| 6498c98 | Denis Yuen | 19 September 2017, 21:50:38 UTC | Merge tag '1.2.10' into develop [maven-release-plugin] copy for tag 1.2.10 | 19 September 2017, 21:50:38 UTC |
| 29e0ee6 | Denis Yuen | 19 September 2017, 21:43:38 UTC | [maven-release-plugin] prepare release 1.2.10 | 19 September 2017, 21:43:38 UTC |
| 25e37fa | Gary Luu | 19 September 2017, 21:30:31 UTC | Secondary files utility test (#903) * Remove more streams just in case, prevent merge input secondary files when there's multiple * Actually check if the secondary files utility is working correctly | 19 September 2017, 21:30:31 UTC |
| 3166a2f | Gary Luu | 19 September 2017, 19:20:27 UTC | Fix for launch with cwltools in tools/workflows (#845) (#900) * Fix for launch with cwltools in tools/workflows * Pull request suggestion | 19 September 2017, 19:20:27 UTC |
| 6000531 | Gary Luu | 02 August 2017, 17:40:23 UTC | Fix for launch with cwltools in tools/workflows (#845) * Fix for launch with cwltools in tools/workflows * Pull request suggestion | 19 September 2017, 14:19:12 UTC |
| 78630b4 | Gary Luu | 19 September 2017, 14:10:06 UTC | Concurrency secondary files fix (#899) * Revert back to using stream() * Add test for concurrency issue | 19 September 2017, 14:10:06 UTC |
| e33fbad | Denis Yuen | 18 September 2017, 14:23:50 UTC | Merge tag '1.2.9' into develop [maven-release-plugin] copy for tag 1.2.9 | 18 September 2017, 14:23:50 UTC |
| dc03976 | Denis Yuen | 18 September 2017, 14:17:41 UTC | Merge branch 'hotfix/1.2.9' | 18 September 2017, 14:17:41 UTC |
| fe4f3d1 | Denis Yuen | 18 September 2017, 14:12:22 UTC | [maven-release-plugin] prepare for next development iteration | 18 September 2017, 14:12:22 UTC |
| 877ef7e | Denis Yuen | 18 September 2017, 14:12:17 UTC | [maven-release-plugin] prepare release 1.2.9 | 18 September 2017, 14:12:17 UTC |
| 425c706 | Denis Yuen | 18 September 2017, 14:09:10 UTC | Fix 1.2.9 provisioning (#891) * Add one type of class casting error * Add mini test for bcbio example of output with nested arrays * Fix incorrect cast structure and add VM kill guard | 18 September 2017, 14:09:10 UTC |
| 904e8d3 | Gary Luu | 15 September 2017, 21:19:45 UTC | Put schema salad version in schema sald version error (#894) | 15 September 2017, 21:19:45 UTC |
| c9deeed | garyluu | 13 September 2017, 17:50:06 UTC | Handle './' paths and never copy the datastore directory | 13 September 2017, 20:48:55 UTC |
| c7eedae | Denis Yuen | 13 September 2017, 17:23:20 UTC | Merge tag '1.2.8' into develop [maven-release-plugin] copy for tag 1.2.8 | 13 September 2017, 17:23:20 UTC |
| d7b105c | Denis Yuen | 13 September 2017, 17:19:28 UTC | Merge branch 'hotfix/1.2.8' | 13 September 2017, 17:19:28 UTC |
| bc84af1 | Denis Yuen | 13 September 2017, 17:14:21 UTC | [maven-release-plugin] prepare for next development iteration | 13 September 2017, 17:14:21 UTC |
| 74f46da | Denis Yuen | 13 September 2017, 17:14:17 UTC | [maven-release-plugin] prepare release 1.2.8 | 13 September 2017, 17:14:17 UTC |
| 427aefe | Denis Yuen | 13 September 2017, 17:11:46 UTC | Get ready for Maven release:prepare | 13 September 2017, 17:11:46 UTC |
| 25c1b66 | Gary Luu | 13 September 2017, 17:06:14 UTC | Changing to not use absolute path, plenty use absolute already (#880) * Changing to not use absolute path, plenty use absolute already * Give this a shot and rebuild both parts of the PR | 13 September 2017, 17:06:14 UTC |
| f1425bd | Denis Yuen | 13 September 2017, 14:41:39 UTC | Give this a shot and rebuild both parts of the PR | 13 September 2017, 17:06:02 UTC |
| 0baa9df | garyluu | 12 September 2017, 15:21:52 UTC | Use new version of cwlavro that handles the default property | 12 September 2017, 15:21:52 UTC |
| 68286ca | garyluu | 12 September 2017, 15:21:30 UTC | More efficient cwl parsing | 12 September 2017, 15:21:30 UTC |
| 5e4dc74 | Denis Yuen | 11 September 2017, 20:45:26 UTC | Iterate version numbers | 11 September 2017, 20:45:26 UTC |
| 1c29cba | Gary Luu | 11 September 2017, 19:50:31 UTC | Use default version when tag is null (#879) | 11 September 2017, 19:50:31 UTC |
| f85dfc2 | Gary Luu | 11 September 2017, 19:50:12 UTC | Feature/indexing (#871) * Changed postgresql driver version * Update index when changing labels * Remove redundant method * Check if entry is published * Add indexing to a bunch of endpoints that ensure the tool already exists * Fix checkstyle * Codestyle and bug fixes * Add re-index to a bunch more inputs in dockertag * Code cleanup with delete/add document functionality * Indexing for workflows * Refactor for tool/workflow index update * Add index update on refresh all tool/workflows * Fix for tests * Changed to use enum * Made a note about updating only the entries that changed | 11 September 2017, 19:50:12 UTC |
| 03884d4 | Denis Yuen | 11 September 2017, 19:37:50 UTC | Merge branch 'hotfix/1.2.7' | 11 September 2017, 19:37:50 UTC |
| 4786e5f | garyluu | 06 September 2017, 17:12:10 UTC | [maven-release-plugin] rollback the release of dockstore-1.2.7-beta | 06 September 2017, 17:12:10 UTC |
| 47c23a3 | garyluu | 06 September 2017, 15:49:33 UTC | [maven-release-plugin] prepare for next development iteration | 06 September 2017, 15:49:33 UTC |
| 0ebd71f | garyluu | 06 September 2017, 15:49:29 UTC | [maven-release-plugin] prepare release dockstore-1.2.7-beta | 06 September 2017, 15:49:29 UTC |
| 94227b0 | garyluu | 05 September 2017, 20:22:03 UTC | Ignore bunny case and ignore client for now | 05 September 2017, 20:27:25 UTC |
| b61a568 | Denis Yuen | 18 August 2017, 20:53:19 UTC | Fix as discussed due relative path to parameter file | 05 September 2017, 19:26:34 UTC |
| 92c1bc5 | Denis Yuen | 18 August 2017, 20:11:18 UTC | Odd | 05 September 2017, 19:26:27 UTC |
| e04225d | Denis Yuen | 18 August 2017, 18:09:11 UTC | Fix up merge and odd relative path issue | 05 September 2017, 19:26:17 UTC |
| b4e6913 | Denis Yuen | 18 August 2017, 20:53:19 UTC | Fix as discussed due relative path to parameter file | 18 August 2017, 20:53:19 UTC |
| 1ee1902 | Denis Yuen | 18 August 2017, 20:11:18 UTC | Odd | 18 August 2017, 20:11:18 UTC |
| d886bf4 | Denis Yuen | 18 August 2017, 18:17:19 UTC | [maven-release-plugin] prepare for next development iteration | 18 August 2017, 18:17:19 UTC |
| 2da8430 | Denis Yuen | 18 August 2017, 18:17:15 UTC | [maven-release-plugin] prepare release 1.3.0-alpha.2 | 18 August 2017, 18:17:15 UTC |
| 5391821 | Denis Yuen | 18 August 2017, 18:09:11 UTC | Fix up merge and odd relative path issue | 18 August 2017, 18:09:11 UTC |
| 1e84f48 | Denis Yuen | 18 August 2017, 18:08:48 UTC | Merge branch 'hotfix/1.2.7' into develop | 18 August 2017, 18:08:48 UTC |
| cfe053c | Denis Yuen | 18 August 2017, 17:13:04 UTC | [maven-release-plugin] prepare for next development iteration | 18 August 2017, 17:13:04 UTC |
| 471f72e | Denis Yuen | 18 August 2017, 17:12:58 UTC | [maven-release-plugin] prepare release 1.2.6 | 18 August 2017, 17:12:58 UTC |
| de630df | Denis Yuen | 18 August 2017, 17:10:49 UTC | Redo release | 18 August 2017, 17:10:49 UTC |
| b487901 | Gary Luu | 18 August 2017, 15:00:02 UTC | Workflow path backport take2 (#870) * Feature/swagger fix (#843) * Use swagger 2.2.3 to generate quay code * Prevent new Jackson from being registered * Test clean up * Generated API change * Implement fix for #814 * Pin ruaeml version (#859) * Inital fix for secondary file provisioning with new test and old test changes * Handle --entry descriptors * Use config file and change file locations * Handle secondary files by converting to absolute path * Handle array of array of files * Retain old secondary files feature * Script to override failed file provisioning * Changed working directory to test parameter file parent * Automatically move secondary files in tool descriptor into the root workflow * Fix up changes due to older codebase * Added a test * Simplifying function * Have an extract ID function * Throw exceptions * Instanceof List instead of ArrayList * Moved secondary files relative->absolute path conversion to a function * Add more tests * Add comments, fixed bug * Generify, reformat, updated comments, etc * Update checkstyle to 8.1 to match Intellij warnings * Check whether vfs can handle a scheme before trying to copy to it | 18 August 2017, 15:00:02 UTC |
| b3decdc | Denis Yuen | 18 August 2017, 14:47:34 UTC | [maven-release-plugin] prepare for next development iteration | 18 August 2017, 14:47:34 UTC |
| 1377da1 | Denis Yuen | 18 August 2017, 14:47:30 UTC | [maven-release-plugin] prepare release 1.2.6 | 18 August 2017, 14:47:30 UTC |
| 18e16ba | Denis Yuen | 18 August 2017, 14:41:25 UTC | Iterate version for test release | 18 August 2017, 14:41:25 UTC |
| 7e7d668 | Denis Yuen | 16 August 2017, 18:43:55 UTC | Iterate version numbers | 16 August 2017, 18:43:55 UTC |
| 7c27b31 | Denis Yuen | 14 August 2017, 20:33:46 UTC | Pin ruaeml version (#859) | 14 August 2017, 20:45:50 UTC |
| 231acae | Denis Yuen | 14 August 2017, 20:33:46 UTC | Pin ruaeml version (#859) | 14 August 2017, 20:33:46 UTC |
| a3ba958 | Denis Yuen | 14 August 2017, 13:42:56 UTC | Implement #755 (#857) | 14 August 2017, 13:42:56 UTC |
| a4058f8 | Denis Yuen | 14 August 2017, 13:42:38 UTC | Sort published tools by starring rather than the current undefined order (#856) | 14 August 2017, 13:42:38 UTC |
| ca40161 | Denis Yuen | 09 August 2017, 20:28:11 UTC | Implement fix for #814 | 09 August 2017, 20:28:11 UTC |
| 93d85d0 | Gary Luu | 09 August 2017, 17:03:17 UTC | Feature/advanced indexing (#846) * Generate a bulk tools * Changed some type strings to text for elasticsearch 5.5 * Better exception * Reorganized + function for getting NDJSON from tool ids | 09 August 2017, 17:03:17 UTC |
| 606cab6 | Denis Yuen | 08 August 2017, 16:05:32 UTC | Generated API change | 08 August 2017, 16:05:32 UTC |
| 289ab2f | Gary Luu | 03 August 2017, 13:34:34 UTC | Feature/swagger fix (#843) * Use swagger 2.2.3 to generate quay code * Prevent new Jackson from being registered * Test clean up | 08 August 2017, 15:56:07 UTC |
| 8e23191 | Gary Luu | 03 August 2017, 13:34:34 UTC | Feature/swagger fix (#843) * Use swagger 2.2.3 to generate quay code * Prevent new Jackson from being registered * Test clean up | 03 August 2017, 13:34:34 UTC |
| 077febe | Gary Luu | 02 August 2017, 17:40:23 UTC | Fix for launch with cwltools in tools/workflows (#845) * Fix for launch with cwltools in tools/workflows * Pull request suggestion | 02 August 2017, 17:40:23 UTC |
| 886089c | Gary Luu | 25 July 2017, 13:46:27 UTC | Update to elastic 5.5 mainly by changing string to keyword for regist… (#825) * Update to elastic 5.5 mainly by changing string to keyword for registry/namespace * Update elastic search version in README * Updating commit id * Removing old elastic ui demo | 25 July 2017, 13:46:27 UTC |
| c457c62 | Denis Yuen | 11 July 2017, 22:31:08 UTC | Merge tag '1.2.5' into develop [maven-release-plugin] copy for tag 1.2.5 | 11 July 2017, 22:31:08 UTC |
| 591813b | Denis Yuen | 11 July 2017, 22:29:34 UTC | Merge branch 'hotfix/1.2.5' | 11 July 2017, 22:29:34 UTC |
| 1dd26db | Denis Yuen | 11 July 2017, 22:21:08 UTC | [maven-release-plugin] prepare for next development iteration | 11 July 2017, 22:21:08 UTC |
| c06bfd8 | Denis Yuen | 11 July 2017, 22:21:04 UTC | [maven-release-plugin] prepare release 1.2.5 | 11 July 2017, 22:21:04 UTC |
| c4ab403 | Denis Yuen | 11 July 2017, 22:08:31 UTC | Merge branch 'hotfix/1.2.5' | 11 July 2017, 22:08:31 UTC |
| df4c612 | Denis Yuen | 11 July 2017, 19:24:00 UTC | Fix formatting | 11 July 2017, 19:24:00 UTC |
| 6816ea4 | Denis Yuen | 11 July 2017, 19:20:54 UTC | Adding null guard and fixing typo | 11 July 2017, 19:20:54 UTC |
| 526158b | Denis Yuen | 05 July 2017, 15:35:37 UTC | Revert unnecessary change | 05 July 2017, 15:35:37 UTC |
| 1c17746 | Denis Yuen | 05 July 2017, 14:32:53 UTC | Add doc | 05 July 2017, 14:32:53 UTC |
| 908a043 | Denis Yuen | 04 July 2017, 21:21:28 UTC | Partial indexes require newer postgres | 04 July 2017, 21:21:28 UTC |
| 3140be4 | Denis Yuen | 04 July 2017, 19:42:59 UTC | Format issue | 04 July 2017, 19:42:59 UTC |
| 238252e | Denis Yuen | 04 July 2017, 19:41:01 UTC | Deal with odd duplicate creation issue | 04 July 2017, 19:41:01 UTC |
| 417417e | Denis Yuen | 04 July 2017, 19:37:29 UTC | First part of #777 | 04 July 2017, 19:39:25 UTC |
| f31ec99 | Denis Yuen | 30 June 2017, 14:08:14 UTC | Fix up broken merge (#797) | 30 June 2017, 14:08:14 UTC |
