834cbcc | Denis Yuen | 13 September 2018, 19:35:35 UTC | [maven-release-plugin] prepare release 1.5.1 | 13 September 2018, 19:35:35 UTC |
c3880a6 | Denis Yuen | 13 September 2018, 19:33:21 UTC | Too early | 13 September 2018, 19:33:21 UTC |
3b999fc | Denis Yuen | 13 September 2018, 19:29:35 UTC | Fix nextflow recursive error (#1822) | 13 September 2018, 19:29:35 UTC |
32a60e5 | Charles Overbeck | 13 September 2018, 16:36:53 UTC | Be quieter logging Google token validation errors (#1819) #1817 Only log the stack trace at the debug log level. | 13 September 2018, 16:36:53 UTC |
4f97406 | Denis Yuen | 12 September 2018, 22:14:41 UTC | Iterate versions | 12 September 2018, 22:14:41 UTC |
74d6a4f | Denis Yuen | 12 September 2018, 22:08:18 UTC | Merge branch 'master' into HEAD | 12 September 2018, 22:08:18 UTC |
e4a4347 | Denis Yuen | 12 September 2018, 19:20:24 UTC | [maven-release-plugin] prepare release 1.5.0 | 12 September 2018, 19:20:24 UTC |
9a06f28 | Denis Yuen | 11 September 2018, 20:42:43 UTC | [maven-release-plugin] prepare for next development iteration | 11 September 2018, 20:42:43 UTC |
fdcd2b4 | Denis Yuen | 11 September 2018, 20:42:37 UTC | [maven-release-plugin] prepare release 1.5.0-rc.2 | 11 September 2018, 20:42:37 UTC |
7286fc5 | Charles Overbeck | 11 September 2018, 20:39:19 UTC | Fix owner losing permissions to their own SAM resource (#1809) #1805 Problem was that a new owner policy was being created when adding another owner, and the new owner policy only added the new owner. 1. We don't need to ever create an owner policy explicitly, as SAM is configured for dockstore-tool resource to always create a default owner policy. This is unlike the writer and reader policies, which we do need to explicitly create. 2. The problem originated in that I was passing the list of policies the new user already belonged to ensurePolicyExists(), which would check to see if the owner policy existed, and it wasn't in the list. 3. Two fixes for that, to be safe. 1. Don't ever let ensurePolicyExists() create an owner policy 2. Pass all of a resource's existing policies to ensurePolicyExists, instead of just the ones the new user already belongs to. 4. In doing that, I noticed that initializePermissions was not returning the policy's permissions. 5. Finally, in looking at this, I noticed the setPermission already returns the list of permissions, and WorkflowResource was unnecessarily fetching them again. | 11 September 2018, 20:39:19 UTC |
ef961f8 | Denis Yuen | 11 September 2018, 17:15:18 UTC | [maven-release-plugin] prepare for next development iteration | 11 September 2018, 17:15:18 UTC |
24744ad | Denis Yuen | 11 September 2018, 17:15:10 UTC | [maven-release-plugin] prepare release 1.5.0-rc.1 | 11 September 2018, 17:15:10 UTC |
652012f | Denis Yuen | 11 September 2018, 17:12:34 UTC | Revert "[maven-release-plugin] prepare release 1.5.0-rc.1" This reverts commit 8bf67f01327a53f26f52b1a713fdd0ccbc9222f6. | 11 September 2018, 17:12:34 UTC |
bb81ed8 | Denis Yuen | 11 September 2018, 17:11:35 UTC | Merge branch 'develop' of github.com:ga4gh/dockstore into develop | 11 September 2018, 17:11:35 UTC |
8bf67f0 | Denis Yuen | 11 September 2018, 17:11:12 UTC | [maven-release-plugin] prepare release 1.5.0-rc.1 | 11 September 2018, 17:11:12 UTC |
50875c8 | Andrew Duncan | 11 September 2018, 15:55:29 UTC | Feature/nextflow rna partial fix (#1803) * Fix to allow refresh to resume after invalid config * removed unused imports | 11 September 2018, 15:55:29 UTC |
3571aca | Denis Yuen | 11 September 2018, 15:55:07 UTC | Fix check to avoid null pointer (#1804) * Fix check to avoid null pointer * Fix Bitbucket and tests for changed check | 11 September 2018, 15:55:07 UTC |
5ad004f | Denis Yuen | 07 September 2018, 19:52:57 UTC | [maven-release-plugin] prepare for next development iteration | 07 September 2018, 19:52:57 UTC |
57e1ec1 | Denis Yuen | 07 September 2018, 19:52:51 UTC | [maven-release-plugin] prepare release 1.5.0-rc.0 | 07 September 2018, 19:52:51 UTC |
f577e4e | Denis Yuen | 07 September 2018, 19:47:35 UTC | prototype hosted workflow limits (#1798) * prototype hosted workflow limits * Use limits as a field, check-in tests | 07 September 2018, 19:47:35 UTC |
c7c5efa | Denis Yuen | 05 September 2018, 20:36:47 UTC | Tighten test parameter editing (#1796) | 05 September 2018, 20:36:47 UTC |
63efdd0 | Denis Yuen | 05 September 2018, 17:27:49 UTC | [maven-release-plugin] prepare for next development iteration | 05 September 2018, 17:27:49 UTC |
ff75b75 | Denis Yuen | 05 September 2018, 17:27:44 UTC | [maven-release-plugin] prepare release 1.5.0-beta.6 | 05 September 2018, 17:27:44 UTC |
b96bec5 | Denis Yuen | 05 September 2018, 17:23:39 UTC | Description update to include warning #1717 (#1791) | 05 September 2018, 17:23:39 UTC |
2351c8a | Denis Yuen | 04 September 2018, 14:06:34 UTC | Fix for sorting and filtering (#1785) * Fix for sorting and filtering * Update WorkflowIT.java | 04 September 2018, 14:06:34 UTC |
fa522b1 | Denis Yuen | 31 August 2018, 18:44:12 UTC | [maven-release-plugin] prepare for next development iteration | 31 August 2018, 18:44:12 UTC |
d8c21e8 | Denis Yuen | 31 August 2018, 18:44:02 UTC | [maven-release-plugin] prepare release 1.5.0-beta.5 | 31 August 2018, 18:44:02 UTC |
f647b47 | Denis Yuen | 31 August 2018, 17:36:14 UTC | Feature/secure more (#1782) * Starring unpublished entries not allowed * Describe metadata in swagger * Transfer over tests | 31 August 2018, 17:36:14 UTC |
298c9af | Denis Yuen | 30 August 2018, 15:14:26 UTC | Feature/more refresh fixes (#1781) * Need more ordering for #1777 * Add fix and test for #1779 | 30 August 2018, 15:14:26 UTC |
a1733dc | Andrew Duncan | 30 August 2018, 14:46:23 UTC | Feature/hosted cli fix (#1774) * better dockstore info display * hosted workflow info cli fix * some small cleanup and usability changes | 30 August 2018, 14:46:23 UTC |
cada20e | Denis Yuen | 28 August 2018, 14:10:42 UTC | [maven-release-plugin] prepare for next development iteration | 28 August 2018, 14:10:42 UTC |
96f670a | Denis Yuen | 28 August 2018, 14:10:37 UTC | [maven-release-plugin] prepare release 1.5.0-beta.4 | 28 August 2018, 14:10:37 UTC |
17ef8b7 | Denis Yuen | 28 August 2018, 14:01:12 UTC | Working on refresh issues in some cases (#1762) * Working on #1405 * Add tests for workflows (confident) * tests for tools (less confident, but seems to fix issue) | 28 August 2018, 14:01:12 UTC |
a8820a4 | Denis Yuen | 27 August 2018, 17:21:13 UTC | Fix build (#1767) | 27 August 2018, 17:21:13 UTC |
4f6649b | Charles Overbeck | 27 August 2018, 16:00:30 UTC | On self-destruct, delete user's workflows and tools (#1766) #1697 | 27 August 2018, 16:00:30 UTC |
649cad4 | Gary Luu | 24 August 2018, 19:38:50 UTC | Feature/1240/auto convert yaml (#1760) * Handle yaml files * Add test * Revert Help change (#1255) | 24 August 2018, 19:38:50 UTC |
83bcc83 | Denis Yuen | 24 August 2018, 18:45:04 UTC | Feature/regression (#1757) * Cleanup * Reactivate regression tests | 24 August 2018, 18:45:04 UTC |
d32585d | Charles Overbeck | 24 August 2018, 16:04:39 UTC | Address SAM edge cases (#1759) #1713 1. If a SAM resource was created by another user directly in the SAM API, handles the 409 status code by returning a message indicating user should contact Dockstore admins at discuss.dockstore.org 2. If a SAM resource was created in the SAM API by the same user, but without all 3 policies, create the additional policies as needed. Also got rid of SAM role name constants, since they are duplicates of the policy names. Made writing some code easier. | 24 August 2018, 16:04:39 UTC |
c919257 | Denis Yuen | 22 August 2018, 19:23:37 UTC | [maven-release-plugin] prepare for next development iteration | 22 August 2018, 19:23:37 UTC |
b90ecb6 | Denis Yuen | 22 August 2018, 19:23:31 UTC | [maven-release-plugin] prepare release 1.5.0-beta.3 | 22 August 2018, 19:23:31 UTC |
0e9ca02 | Denis Yuen | 22 August 2018, 17:48:34 UTC | Generate a git-like URL to enable links within dockstore UI for hosted workflows (#1748) * Supporting #1746 | 22 August 2018, 17:48:34 UTC |
0da44c5 | Andrew Duncan | 22 August 2018, 17:47:31 UTC | Feature/nf core workaround (#1749) * Crappy temporary workaround for nf core parsing issue * changed test to test for nf core | 22 August 2018, 17:47:31 UTC |
9df03e4 | Denis Yuen | 22 August 2018, 17:40:59 UTC | Add dates to workflows at create time (#1752) | 22 August 2018, 17:40:59 UTC |
77f0979 | Denis Yuen | 21 August 2018, 20:16:38 UTC | Small fixes (#1750) * Small fixes to RSS feed to improve scalability * RSS feed now needs non null values for testing | 21 August 2018, 20:16:38 UTC |
fd4f975 | Charles Overbeck | 21 August 2018, 19:56:39 UTC | When self-destructing, remove sharing records (#1733) #1719 Add `isSharing` to `PermissionsInterface`. Call it to check if a user can delete herself/himself -- in addition to any other rules, users should not be able to delete themselves if they are sharing workflow(s) with others. Add `selfDestruct` to `PermissionsInterface`, which will delete any sharing records. For SAM, this means that we remove the resourceIds that the user owns. | 21 August 2018, 19:56:39 UTC |
e684e67 | Gary Luu | 21 August 2018, 15:29:58 UTC | Feature/1698/tests (#1736) * initial tests * Refactor * PR changes * PR changes * More assertion | 21 August 2018, 15:29:58 UTC |
e4cf310 | Gary Luu | 20 August 2018, 20:16:46 UTC | Handle unknown runner (#1727) * Handle unknown runner * Show options * Revert this once there's another runner deps to list | 20 August 2018, 20:16:46 UTC |
398eed7 | Denis Yuen | 20 August 2018, 15:21:28 UTC | [maven-release-plugin] prepare for next development iteration | 20 August 2018, 15:21:28 UTC |
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 |