| 6aecc64 | Denis Yuen | 20 August 2018, 15:21:23 UTC | [maven-release-plugin] prepare release 1.5.0-beta.2 | 20 August 2018, 15:21:23 UTC |
| 071fa54 | Denis Yuen | 20 August 2018, 15:18:19 UTC | Missing annotation for dag and tools (#1730) * Missing annotation * Fix permissions checking for test parameter files | 20 August 2018, 15:18:19 UTC |
| fd6f7d7 | Andrew Duncan | 19 August 2018, 02:20:19 UTC | update user object on hosted endpoint call (#1726) * update user object on hosted endpoint call * on username change, invalidate cache and update username in token * test for checking that on username change new hosted workflows use the correct username as org | 19 August 2018, 02:20:19 UTC |
| 78f0a4b | Denis Yuen | 17 August 2018, 18:38:24 UTC | [maven-release-plugin] prepare for next development iteration | 17 August 2018, 18:38:24 UTC |
| a602ec4 | Denis Yuen | 17 August 2018, 18:38:18 UTC | [maven-release-plugin] prepare release 1.5.0-beta.1 | 17 August 2018, 18:38:18 UTC |
| 2a2e545 | Denis Yuen | 17 August 2018, 18:35:35 UTC | Feature/more tests (#1720) * Expand tests to search and use other user * update secret archive * Hook up tests with es * Add curator tests and new confidential migrations | 17 August 2018, 18:35:35 UTC |
| 4fa15e0 | Denis Yuen | 17 August 2018, 18:30:32 UTC | Implement and add tests for hosted workflow metadata (#1725) * Implement and add tests for hosted workflow metadata * Fix up tests now that hosted workflows use metadata * Fix up test via deletion order in DB to avoid constraints | 17 August 2018, 18:30:32 UTC |
| a8a3b53 | Andrew Duncan | 16 August 2018, 20:39:46 UTC | Feature/duplicate hosted entry error (#1722) * ensure that users cannot add hosted entries with duplciate paths | 16 August 2018, 20:39:46 UTC |
| bfa07b4 | Denis Yuen | 16 August 2018, 14:10:23 UTC | Manually suppress jersey logging for zip download (#1715) | 16 August 2018, 14:10:23 UTC |
| 7a74eb9 | Denis Yuen | 16 August 2018, 14:10:09 UTC | Re-use download zip code for unpublished launch (#1710) * Re-use download zip code * also enables proper use of credentials * biggest change was that zip was improperly writing relative paths * Add test for launching hosted workflows * Add tests for #1718 | 16 August 2018, 14:10:09 UTC |
| fed9796 | Denis Yuen | 15 August 2018, 15:17:14 UTC | Login message (#1716) | 15 August 2018, 15:17:14 UTC |
| 5bd725e | Denis Yuen | 14 August 2018, 21:03:17 UTC | Feature/second security pass (#1706) * Fix DAG tests to use authentication since unpublished * Optional security for a pile of endpoints * Add authentication to tool listing for unpublished workflows | 14 August 2018, 21:03:17 UTC |
| 35464bc | Gary Luu | 14 August 2018, 15:56:54 UTC | Simple fix for dev env (#1709) * Simple fix for dev env * Move variable to public constant * Test | 14 August 2018, 15:56:54 UTC |
| a8fd42f | Denis Yuen | 13 August 2018, 21:26:28 UTC | [maven-release-plugin] prepare for next development iteration | 13 August 2018, 21:26:28 UTC |
| 1b92339 | Denis Yuen | 13 August 2018, 21:26:23 UTC | [maven-release-plugin] prepare release 1.5.0-beta.0 | 13 August 2018, 21:26:23 UTC |
| bbf51ea | Denis Yuen | 13 August 2018, 18:40:23 UTC | Remove orphan query | 13 August 2018, 21:23:09 UTC |
| fe20a5a | Denis Yuen | 13 August 2018, 16:49:42 UTC | Not sure why this is in this branch | 13 August 2018, 21:23:09 UTC |
| 3235b48 | Denis Yuen | 13 August 2018, 15:51:35 UTC | Fix self-destruct DAO | 13 August 2018, 21:23:09 UTC |
| ec0ddaa | Denis Yuen | 13 August 2018, 15:51:02 UTC | Laggard cleanup for TRS changes | 13 August 2018, 21:23:09 UTC |
| 446785c | Andrew Duncan | 13 August 2018, 19:51:03 UTC | Feature/nextflow name conversion (#1702) * changed from nextflow to nfl, fixed issue 1662 | 13 August 2018, 19:51:03 UTC |
| a83e107 | Denis Yuen | 10 August 2018, 20:37:26 UTC | [maven-release-plugin] prepare for next development iteration | 10 August 2018, 20:37:26 UTC |
| 67a612c | Denis Yuen | 10 August 2018, 20:37:21 UTC | [maven-release-plugin] prepare release 1.5.0-alpha.10 | 10 August 2018, 20:37:21 UTC |
| 76bd56d | Denis Yuen | 10 August 2018, 20:33:05 UTC | Feature/ga4gh name standard (#1624) Update WS to match TRS release/update https://github.com/ga4gh/tool-registry-service-schemas/pull/48 - allow search for checker workflows - allow meta_version to be optional as suggested in #37 - adds alias suggestion #38 - standardized fields for containerfile, descriptors, and test json for ease of use (breaking, but hopefully simple change for retrieving test or containerfile content directly as opposed to via URL) | 10 August 2018, 20:33:05 UTC |
| d5d44d4 | Denis Yuen | 10 August 2018, 17:08:17 UTC | Feature/rename user (#1694) - working copy of changes for #1691 - includes - extended user data endpoint to determine if a user can be deleted - boolean for user indicating if they've accepted their username - add token endpoints are told by satellizer whether this is a login or register op - profile and token constraints (unique usernames, google and github accounts can only be linked to one account) - change user endpoints - tests for most of the above | 10 August 2018, 17:08:17 UTC |
| 06a60fd | Charles Overbeck | 09 August 2018, 15:51:08 UTC | Add Data Object Service File plugin (#1683) Added release 0.0.1 to plugins.json. Download didn't work, because... HEAD call to `https://github.com/dockstore/data-object-service-plugin/releases/ download/0.0.1/dockstore-file-dos-plugin-0.0.1.zip` was failing(!). This is because when calling srcContent.getSize(), it would ultimately call org.apache.commons.vfs2.provider.http.HttpFileObject.doGetType, which would do a HEAD, and the GitHub API returns a 403. So wrapped call to get the size in a try...catch. If the size doesn't come back, display an indeterminate progress bar. I believe this could fix hypothetical cases where there is no size in the header, e.g, if there is a chunked response. | 09 August 2018, 15:51:08 UTC |
| 0a800db | Andrew Duncan | 08 August 2018, 18:42:28 UTC | Added an endpoint to check if a user with a given name exists (#1692) | 08 August 2018, 18:42:28 UTC |
| d92cc5c | Charles Overbeck | 08 August 2018, 16:18:41 UTC | Properly look up user for calls with Google token (#1689) #1684 When web service gets a call with a Google token, look for an existing user by searching User.Profile for that email address. | 08 August 2018, 16:18:41 UTC |
| f84ab6d | Gary Luu | 07 August 2018, 18:44:21 UTC | Replace all (#1686) * Replace all * Fix * Removed unused imports * Revert TRS change | 07 August 2018, 18:44:21 UTC |
| bc4ad8a | Denis Yuen | 03 August 2018, 20:12:19 UTC | [maven-release-plugin] prepare for next development iteration | 03 August 2018, 20:12:19 UTC |
| 734228b | Denis Yuen | 03 August 2018, 20:12:14 UTC | [maven-release-plugin] prepare release 1.5.0-alpha.9 | 03 August 2018, 20:12:14 UTC |
| dbfc122 | Gary Luu | 03 August 2018, 20:09:03 UTC | Feature/1370/token check (#1676) * Add migration from token foreign key with test * Cleaner way of displaying login * Update comment, fix test * Add tests * Delete tokens first * Add id * PR changes | 03 August 2018, 20:09:03 UTC |
| 5e4b381 | Denis Yuen | 03 August 2018, 17:24:30 UTC | Feature/security check, catch of the day (#1682) * Remove archaic and redundant endpoints to reduce surface * First catch, hosted workflows can be truly private * test that their contents cannot be retrieved * cleanup freemarker dependencies | 03 August 2018, 17:24:30 UTC |
| 33df383 | Andrew Duncan | 03 August 2018, 17:19:52 UTC | Feature/nextflow dag extension (#1677) * some basics working for nextflow parsing * use default container from config for processes | 03 August 2018, 17:19:52 UTC |
| 185fe72 | Denis Yuen | 03 August 2018, 13:59:55 UTC | Try random order for some modules and re-run flaky tests once (#1678) * Try random order and re-run flaky tests once * Turn off randomness just for integration test module * Quiet the GA4GH tests | 03 August 2018, 13:59:55 UTC |
| b0ea911 | Denis Yuen | 02 August 2018, 14:31:06 UTC | Elaborate on error messages (#1675) | 02 August 2018, 14:31:06 UTC |
| ea3bb6d | Denis Yuen | 02 August 2018, 14:03:42 UTC | Hook up hosted workflows and old list format for CWL (#1674) * Hook up hosted workflows and old list format for CWL * a test for both situations * also cleans up DAO passing to web resource classes | 02 August 2018, 14:03:42 UTC |
| 0fe6f5c | Denis Yuen | 02 August 2018, 14:02:35 UTC | Fixup path oddity for zip files (#1672) * Fixup path oddity for zip files | 02 August 2018, 14:02:35 UTC |
| e24a5e5 | Charles Overbeck | 01 August 2018, 17:06:30 UTC | Correct Check for Original Owner (#1666) * Correct Check for Original Owner #1657 Problem was that I was comparing email with User.username, which will not be the Google email, if the user first signed in with GitHub. Now also check profile for an email in there. Also: * Add the check when adding a permission; originally only checked when removing a permission. Basically we shouldn't let you muck with an original owner's permissions at all. | 01 August 2018, 17:06:30 UTC |
| f846654 | Gary Luu | 01 August 2018, 13:47:25 UTC | Feature/update user metadata (#1652) * Update user profile upon token creation * Move things around for easier mocking * Add resource test * Also check that for profile updates * Simplify * Fix formatting * Most PR changes * More specific mock * Better assertions * Integration test mocks interaction with Google * Add assertions for user profiles * Fix | 01 August 2018, 13:47:25 UTC |
| 61a752d | Denis Yuen | 31 July 2018, 19:09:59 UTC | Properly name zip file (#1667) * Properly name zip file | 31 July 2018, 19:09:59 UTC |
| a352298 | Denis Yuen | 30 July 2018, 18:25:01 UTC | Feature/entry cleanup (#1659) * cleanup * Are part of our gitlab tests disabled? | 30 July 2018, 18:25:01 UTC |
| 87889e7 | Denis Yuen | 27 July 2018, 15:08:12 UTC | [maven-release-plugin] prepare for next development iteration | 27 July 2018, 15:08:12 UTC |
| 9608843 | Denis Yuen | 27 July 2018, 15:08:04 UTC | [maven-release-plugin] prepare release 1.5.0-alpha.8 | 27 July 2018, 15:08:04 UTC |
| 03a37a1 | Charles Overbeck | 27 July 2018, 15:01:46 UTC | Set PluginManager system version (#1655) #1629 Allows the data object service file plugin, which has its requires set to `>0.0.0` to get loaded by this version of Dockstore. Older versions of Dockstore, which have the system version set to 0.0.0, will not load that plugin. | 27 July 2018, 15:01:46 UTC |
| 9793586 | Denis Yuen | 27 July 2018, 15:01:06 UTC | Add tool, workflow download for CLI (#1653) * adds tests * re-use code for checker workflow download | 27 July 2018, 15:01:06 UTC |
| d018ad3 | Charles Overbeck | 26 July 2018, 15:37:57 UTC | Remove existing permissions when setting a new one (#1643) Issue #1625 | 26 July 2018, 15:37:57 UTC |
| 1c2ec54 | Andrew Duncan | 26 July 2018, 14:56:11 UTC | properly authenticate zip (#1636) | 26 July 2018, 14:56:11 UTC |
| ce459b3 | Denis Yuen | 26 July 2018, 14:14:13 UTC | Test just in case (#1647) * Test just in case * Check for additional case * Expand description javadoc | 26 July 2018, 14:14:13 UTC |
| ee7ee09 | Charles Overbeck | 25 July 2018, 23:06:07 UTC | Add endpoint for users to get their actions (#1638) * Add endpoint for users to get their actions #1589 The issue in the ticket was because the UI was comparing the GitHub username with the Google email address that came back from the permissions call. That, plus the fact that I had forgotten about SAM's support for groups, means we do need an endpoint to indicate the actions a user can perform on workflow. I had this before, with OPTIONS operations on a few API calls, but it was clunky and overkill, so I've added a new endpoint, `/path/workflow/{repository}/actions`, that returns the actions a user can perform on a workflow. The issue with groups is that a user can be given permissions to a resource through a group -- in that case the user's individual email will not show up in the list of permissions. So we could not tell client-side what a user's permissions are just by reading the email addresses. Also: * Added Not Implemented to state changing operations in NoOpPermissionsImpl, just in case it gets turned on and somebody tries to use it. | 25 July 2018, 23:06:07 UTC |
| a41bbde | Denis Yuen | 25 July 2018, 17:51:30 UTC | Feature/generated version num (#1641) | 25 July 2018, 17:51:30 UTC |
| b3733f9 | Denis Yuen | 25 July 2018, 15:48:49 UTC | Feature/api update (#1640) * Lay groundwork for configurable swagger-ui generation * update secret archive * Port should be optional * Cleanup and tighten up a few checks while at it | 25 July 2018, 15:48:49 UTC |
| 8d3a94a | Denis Yuen | 24 July 2018, 14:28:10 UTC | Implement filtered count (#1635) * Implement filtered count | 24 July 2018, 14:28:10 UTC |
| bd3fe5c | Gary Luu | 23 July 2018, 19:08:20 UTC | Feature/verification (#1623) * Migrate legacy verified information * Pin TRS yaml to a specific commit * Add tests * Fix comment | 23 July 2018, 19:08:20 UTC |
| c5ba06e | Charles Overbeck | 23 July 2018, 16:45:42 UTC | Fix typos in permissions endpoints. (#1632) | 23 July 2018, 16:45:42 UTC |
| 01880f9 | Denis Yuen | 20 July 2018, 14:54:12 UTC | [maven-release-plugin] prepare for next development iteration | 20 July 2018, 14:54:12 UTC |
| faf83f0 | Denis Yuen | 20 July 2018, 14:54:07 UTC | [maven-release-plugin] prepare release 1.5.0-alpha.7 | 20 July 2018, 14:54:07 UTC |
| 330821e | Denis Yuen | 19 July 2018, 21:08:07 UTC | Merge branch 'develop' of github.com:ga4gh/dockstore into develop | 19 July 2018, 21:08:07 UTC |
| e7c4c75 | Denis Yuen | 19 July 2018, 20:56:47 UTC | Feature/download workflow zip (#1620) * added download workflow zip endpoint * changed to using built in zip utility and streaming * added download zip for tools | 19 July 2018, 20:56:47 UTC |
| 52db91f | Denis Yuen | 19 July 2018, 18:55:33 UTC | Optional auth for TRS endpoints (#1614) * includes tests and mustache template changes | 19 July 2018, 18:55:33 UTC |
| 826ec05 | Charles Overbeck | 19 July 2018, 15:10:05 UTC | Don't Return Duplicate Shared Workflows (#1618) * Don't Return Duplicate Shared Workflows #1609 In SAM, for the same resource id, the same email can be added to more than one policy for that resource. That would lead to the same workflow showing up more than once, each time for a different role, on the shared flows endpoint. Now weed out duplicates by only returning the resource of the most privileged role. | 19 July 2018, 15:10:05 UTC |
| 5617ece | Denis Yuen | 18 July 2018, 14:28:08 UTC | Pin TRS yaml to a specific commit | 18 July 2018, 15:24:13 UTC |
| b9dc47f | Denis Yuen | 17 July 2018, 15:40:53 UTC | Feature/wdl launch and convert fix (#1611) * properly provision wdl nested imports * No need to edit wdl descriptors after downloading, instead use relative paths from primary descriptor * Match expected behaviour from https://github.com/broadinstitute/cromwell/issues/3868 * Move test resources to match | 17 July 2018, 15:40:53 UTC |
| fea295f | Charles Overbeck | 16 July 2018, 17:58:10 UTC | Change Permissions API (#1610) * Change Permissions API Fixes #1605, which in turn fixes #1589 * Get rid of OPTIONS endpoints for querying permissions * Rolled back change to swagger-java-client which enabled OPTIONS * The `/path/workflow/{repository}/permissions` endpoint would previously fail if you weren't an owner. Now: * If you are an owner, returns all permissions for the workflow * If you have non-owner permissions on the workflow, returns only your permission. * If you have no permission on the workflow, returns 403 * In SAM, since only an owner can get the permissions, derive the current user's permission by seeing what actions she can do. * InMemoryPermissionsImpl wasn't following the contract very closely, e.g., anybody could have set a permission; now it forces you to be an owner | 16 July 2018, 17:58:10 UTC |
| d2a7de4 | Denis Yuen | 16 July 2018, 14:26:42 UTC | Set last modified date across all source control and hosted (#1606) | 16 July 2018, 14:26:42 UTC |
| eb78c47 | Charles Overbeck | 13 July 2018, 15:00:31 UTC | Return empty map of shared workflows if not in SAM (#1602) Fixes #1597 If user is unauthorized in SAM, e.g., you have a Google token but haven't registered with FireCloud, you will get a 401 making SAM API calls. In that case, just return an empty map instead of throwing an exception, as that is legitimate. | 13 July 2018, 15:00:31 UTC |
| 4f707f6 | Denis Yuen | 12 July 2018, 19:53:18 UTC | [maven-release-plugin] prepare for next development iteration | 12 July 2018, 19:53:18 UTC |
| 557f544 | Denis Yuen | 12 July 2018, 19:53:12 UTC | [maven-release-plugin] prepare release 1.5.0-alpha.6 | 12 July 2018, 19:53:12 UTC |
| b221eb3 | Charles Overbeck | 12 July 2018, 19:47:25 UTC | Permissions API Cleanup (#1592) * Permissions API Cleanup Fixes #1582 Original owners are what Workflow.getUsers() returns. These are the users who created the hosted workflow or belong to the GitHub repo of a workflow. This commit resolves those users with users who have been authorized via SAM, users that sometimes overlap, as well as other issues. * Don't allow "original owners" to remove themselves as owners. * Also return "original owners" when fetching permissions. * When returning shared workflows, don't return workflows that you are an original owner of. * If you are not an owner of a workflow, the request to get permissions for that workflow now fails * If you are not logged in with Google, requesting workflows shared with you know returns an empty map instead of a 401. * Change check for audience to only be prefix * Changed signature of setPermission so the parameter order is consistent with other methods in the interface. | 12 July 2018, 19:47:25 UTC |
| 01ce300 | Gary Luu | 11 July 2018, 20:26:30 UTC | Pull in commit dates for Bitbucket (#1586) * Pull in commit dates for Bitbucket * PR changes * Fix | 11 July 2018, 20:26:30 UTC |
| eb7eb4a | Denis Yuen | 10 July 2018, 17:20:23 UTC | Attempted merge (#1583) for hotfix 1.4.5 | 10 July 2018, 17:20:23 UTC |
| 6c9771c | Denis Yuen | 10 July 2018, 17:19:45 UTC | Make serialized collection order deterministic (#1579) * Make serialized collection order deterministic * Fix comparable * Add a test for sort order | 10 July 2018, 17:19:45 UTC |
| a048c27 | Gary Luu | 10 July 2018, 17:16:53 UTC | Feature/pagination change (#1577) * Pagination change required * Allow X-total-count in workflow resource * Change default for workflow too * Update yamls | 10 July 2018, 17:16:53 UTC |
| b9ab768 | Gary Luu | 10 July 2018, 17:16:19 UTC | Move repo to dockstore-testing (#1585) | 10 July 2018, 17:16:19 UTC |
| 67c81c6 | Andrew Duncan | 09 July 2018, 20:45:56 UTC | Feature/hosted entry default version (#1534) New endpoint for setting the default version of tools and workflows, instead of being lumped together with update. | 09 July 2018, 20:45:56 UTC |
| 41d9c78 | Denis Yuen | 09 July 2018, 15:32:41 UTC | Feature/labels check (#1574) * Implement check for permissions for labels * Add test * Make tests more stringent * @Test(expected=ApiException.class) is a bit of an antipattern | 09 July 2018, 15:32:41 UTC |
| 128e44a | Denis Yuen | 09 July 2018, 14:27:58 UTC | Properly catch wdl syntax exception (#1578) | 09 July 2018, 14:27:58 UTC |
| 8a7093f | Charles Overbeck | 07 July 2018, 01:09:42 UTC | Accept Google tokens from users not in Dockstore (#1566) * Accept Google tokens from users not in Dockstore If API call made with a Google token not issued against the Dockstore audience (client id), accept it if it's issued against a whitelisted Google client id (see DockstoreWebserviceConfiguration.externalGoogleClientIds). If the user is not in Dockstore, create the user. The main difference for a User created this way vs. a user signing in is that there is no refresh token. Added org.mockito.plugins.MockMaker file so I could mock Userinfoplus, a final class, which Mockito doesn't let you mock by default. | 07 July 2018, 01:09:42 UTC |
| 042875e | Denis Yuen | 05 July 2018, 21:29:01 UTC | A couple coarse guards for inappropriate content (#1568) * A few coarse guards for #1536 | 05 July 2018, 21:29:01 UTC |
| 1a85936 | Denis Yuen | 05 July 2018, 15:40:01 UTC | Feature/grab bag (#1571) * Quick fix for #1541 * Add check for #801 * Fix glitch with being unable to change workflow type | 05 July 2018, 15:40:01 UTC |
| 8ec5e94 | Charles Overbeck | 05 July 2018, 15:03:14 UTC | For shared flows, don't show roles without workflows (#1567) If a SharedWorkflows object has no workflows, don't return it. This can happen if workflowDAO.findByPath doesn't find the any of the workflows for a given role. I believe this is an unlikely scenario, but I've seen it an a dev environment where I register a resource with SAM, then effectively delete the resource by reinitializing my database, so that SAM ends up pointing to a resource that doesn't exist. | 05 July 2018, 15:03:14 UTC |
| 611d78e | Denis Yuen | 03 July 2018, 18:50:40 UTC | Move away from Bitbucket v1 to v2 (#1565) * Move away from Bitbucket v1 to v2 * also use swagger * their swagger is broken for codegen due to https://github.com/swagger-api/swagger-codegen/issues/5562 | 03 July 2018, 18:50:40 UTC |
| 54ab051 | Gary Luu | 29 June 2018, 17:41:25 UTC | Feature/1194/git lab dates (#1563) * Add date modified to gitlab workflow versions * Add assertion and enable GitLab test * Fix comment | 29 June 2018, 17:41:25 UTC |
| a95257b | Denis Yuen | 29 June 2018, 17:17:53 UTC | Feature/nextflow secondary files (#1561) * Secondary files working locally * limitations * 10 files per directory for bitbucket * noticed Bitbucket issue, tracked as #1552 * Add tests for nextflow, also tests bitbucket * need to figure out situation with gitlab | 29 June 2018, 17:17:53 UTC |
| 991ce3b | Andrew Duncan | 29 June 2018, 14:57:56 UTC | Release/1.5.0 alpha.5 (#1562) * [maven-release-plugin] prepare release 1.5.0-alpha.5 * [maven-release-plugin] prepare for next development iteration | 29 June 2018, 14:57:56 UTC |
| 44d1f4b | Charles Overbeck | 28 June 2018, 20:55:28 UTC | Change /workflows/sharedworkflow response entity (#1547) Fixes #1532 Now returns a List<SharedWorkflows> instead of List<Workflow>, where SharedWorkflows class has a Role and a list of workflows. Initially attempted to have the endpoint return a Map<Role, List<Workflow>>, but the problem when I do that is that the generated Swagger Java client returns a Map<Role, Object>. This response is slightly more cumbersome, but it preserves the types in the Swagger clients, so it seems better. | 28 June 2018, 20:55:28 UTC |
| 1ae9836 | Andrew Duncan | 28 June 2018, 20:08:25 UTC | Feature/permissions existing endpoints (#1558) * update some endpoints for workflows so that they handle permissions * extended test for hosted wf permissions | 28 June 2018, 20:08:25 UTC |
| c9dd9b4 | Charles Overbeck | 28 June 2018, 17:13:00 UTC | Make swagger2openapi run on Mac (#1556) Fixes #1529. Use the -n option for quietness. It works on both Linux (Ubuntu 18.04) and Mac. Needed the two forward slashes at the beginning of line 14, otherwise the file ends up with extra indentation on Ubuntu (but not on Mac OS). Compared the results of running on Ubuntu before and after my change, and the output was identical. | 28 June 2018, 17:13:00 UTC |
| 9d68592 | Denis Yuen | 28 June 2018, 16:05:15 UTC | swagger-kongchen plugin update and reader switch (#1550) * WIP for #1530 * swagger.yaml changes due to 3.1.7 and more authentic swagger reader | 28 June 2018, 16:05:15 UTC |
| 7b6c631 | Denis Yuen | 27 June 2018, 20:53:16 UTC | Working pagination prototype (#1535) * Working pagination prototype * Add sorting, order by, and tests | 27 June 2018, 20:53:16 UTC |
| 63ff10b | Denis Yuen | 27 June 2018, 20:50:35 UTC | Test without bunny (#1546) | 27 June 2018, 20:50:35 UTC |
| 5fb3133 | Gary Luu | 27 June 2018, 18:20:06 UTC | Feature/1370/merge google GitHub (#1508) * Merge google and github accounts * Renamed * Query param for update user metadata * Use emails as unique identifier * Break out google info into seperate table * Use embeddable profile * Move profile to another table * Update Swagger and OpenAPI * Name unique constraint name * Fix for file format changes in Git repo * Swagger description change * Renamed profiles, create basic user * Add avatar url back * Removed basic user * Fix swagger.yaml * Always eagerly load yourself * Changing tests for new implementation * Update google access token | 27 June 2018, 18:20:06 UTC |
| 2540b76 | Charles Overbeck | 23 June 2018, 02:48:57 UTC | Start sharing implementation (#1477) Random notes: * Three implementations: * NoOp, which does no sharing, in case we need to turn off * InMemory, which is transient; useful for unit/integration testing * Sam, which delegates to SAM * Added some OPTIONS endpoints, so that UI can see what operations are permitted. * Generated Swagger Java client does not support OPTIONS, so added ApiClient.mustache. | 23 June 2018, 02:48:57 UTC |
| 2a51ae2 | Denis Yuen | 22 June 2018, 18:39:40 UTC | Implement TRS changes including aliases and search by ID (#1506) * Enable TRS tests without adding client tests * Fix tool id search * Update swagger ui * TRS search for checker workflows * Allow for checker search * Add null implementation of aliases * Add aliases addition in Dockstore and exposed via TRS | 22 June 2018, 18:39:40 UTC |
| b9d7fe3 | Gary Luu | 22 June 2018, 13:31:31 UTC | Feature/1220/deps help (#1523) * Add help to 'dockstore --help' * Make optional by using default | 22 June 2018, 13:31:31 UTC |
| f83c036 | Denis Yuen | 20 June 2018, 18:18:25 UTC | Disable unreliable test | 21 June 2018, 15:42:19 UTC |
| 418e742 | Denis Yuen | 19 June 2018, 21:01:44 UTC | Make swagger2open.sh a bit more quiet | 21 June 2018, 15:42:19 UTC |
| 7573716 | Denis Yuen | 21 June 2018, 14:29:57 UTC | Feature/code cov stage test (#1525) * Try using flags #1507 * Try removing dashes from variable name | 21 June 2018, 14:29:57 UTC |
| 186d42a | Denis Yuen | 21 June 2018, 14:24:16 UTC | Update template for decrypt script (#1527) * Update template for decrypt script | 21 June 2018, 14:24:16 UTC |
| 26acdd4 | Denis Yuen | 20 June 2018, 19:36:36 UTC | strip content from all logged in workflows and tools (#1521) * strip content from all logged in workflows and tools | 20 June 2018, 19:36:36 UTC |
| a4e9854 | Denis Yuen | 20 June 2018, 15:10:38 UTC | Stop failing builds for minor decreases in coverage (#1522) | 20 June 2018, 15:10:38 UTC |
