https://github.com/ga4gh/dockstore

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Revision Author Date Message Commit Date
fbc9a7a [maven-release-plugin] prepare release 1.6.0-alpha.0 07 November 2018, 16:05:43 UTC
f9f479e Feature/ng2 ui auth (#1871) * Adjust for new ng2-ui-auth * Update satellizerjson in tests * Use fixtures 07 November 2018, 15:31:16 UTC
66c2d77 feature/recreate-github-token Minor text changes to bad HTTP request message (#1874) * Minor text changes describing github token recreation process 02 November 2018, 20:15:54 UTC
7abc249 Feature/shared-workflows-improvement dynamic query (#1866) * Fetches shared workflows in bulk rather than 1-by-1 * Creates a dynamic query of workflows using CriteriaBuilder * Extracts map returned by `workflowsSharedWithUser` to avoid duplicate calls to the external service * Adds additional filters to workflows returned by `findByPaths` * Adds additional integration tests for a user with two shared workflows 01 November 2018, 20:29:42 UTC
5a34a9c Feature/dos-file-provision set configuration added to PreProvisionInterface (#1867) * Adds default setConfiguration() method to PreProvisionInterface * Updates Plugin Manager system version to 0.0.2, which allows plugins implementing new PreProvisionInterface to be loaded by Dockstore * Older versions of Dockstore w/ system version less than 0.0.2 will not load plugins with requirements '>0.0.1' * Extracts method for finding name of a plugin in FileProvisioning class * Provides test for above method 31 October 2018, 20:11:24 UTC
deeaa62 Java 10 support and testing (#1837) * Update .travis.yml * Looks like needed for Java 8 due to swagger codegen https://github.com/kongchen/swagger-maven-plugin/issues/560 * Need to upgrade Maven See https://github.com/travis-ci/travis-ci/issues/7719 * Upgrade mockito to avoid ByteBuddy error * see https://github.com/mockito/mockito/issues/1298 * Fix for Jersey-JAXB issue * see https://github.com/dropwizard/dropwizard/issues/2318 * Java 10 requires Dropwizard update * Looks like spotbugs replaces findbugs for Java 9 support * see https://github.com/gradle/gradle/issues/720 * Run regression tests in Java 8, a bunch of mocking issues * https://github.com/powermock/powermock/issues/783 * https://github.com/powermock/powermock/issues/864 * Workaround https://github.com/trautonen/coveralls-maven-plugin/issues/112 25 September 2018, 17:03:17 UTC
3c8bbec Feature/1240/tool wdl yaml (#1797) * Let --yaml work with wdl tools * Add test 25 September 2018, 13:56:58 UTC
b96e87c Feature/security review (#1810) * list public workflow versions should use findPublishedById * some cleanup of swagger comments/notes 24 September 2018, 14:07:24 UTC
bfb7392 update secret archive 17 September 2018, 20:19:14 UTC
6167c43 Remove un-used risky WDL code 17 September 2018, 20:19:14 UTC
40c5cca Remove code replaced by compose_setup 17 September 2018, 20:19:14 UTC
78cb90a Merge tag '1.5.1' into develop [maven-release-plugin] copy for tag 1.5.1 13 September 2018, 19:41:28 UTC
834cbcc [maven-release-plugin] prepare release 1.5.1 13 September 2018, 19:35:35 UTC
c3880a6 Too early 13 September 2018, 19:33:21 UTC
3b999fc Fix nextflow recursive error (#1822) 13 September 2018, 19:29:35 UTC
32a60e5 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 Iterate versions 12 September 2018, 22:14:41 UTC
74d6a4f Merge branch 'master' into HEAD 12 September 2018, 22:08:18 UTC
8a084dc Typo 12 September 2018, 22:02:52 UTC
9d1fbc4 [maven-release-plugin] prepare for next development iteration 12 September 2018, 19:20:29 UTC
e4a4347 [maven-release-plugin] prepare release 1.5.0 12 September 2018, 19:20:24 UTC
9a06f28 [maven-release-plugin] prepare for next development iteration 11 September 2018, 20:42:43 UTC
fdcd2b4 [maven-release-plugin] prepare release 1.5.0-rc.2 11 September 2018, 20:42:37 UTC
7286fc5 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 [maven-release-plugin] prepare for next development iteration 11 September 2018, 17:15:18 UTC
24744ad [maven-release-plugin] prepare release 1.5.0-rc.1 11 September 2018, 17:15:10 UTC
652012f Revert "[maven-release-plugin] prepare release 1.5.0-rc.1" This reverts commit 8bf67f01327a53f26f52b1a713fdd0ccbc9222f6. 11 September 2018, 17:12:34 UTC
bb81ed8 Merge branch 'develop' of github.com:ga4gh/dockstore into develop 11 September 2018, 17:11:35 UTC
8bf67f0 [maven-release-plugin] prepare release 1.5.0-rc.1 11 September 2018, 17:11:12 UTC
50875c8 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 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 [maven-release-plugin] prepare for next development iteration 07 September 2018, 19:52:57 UTC
57e1ec1 [maven-release-plugin] prepare release 1.5.0-rc.0 07 September 2018, 19:52:51 UTC
f577e4e 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 Tighten test parameter editing (#1796) 05 September 2018, 20:36:47 UTC
63efdd0 [maven-release-plugin] prepare for next development iteration 05 September 2018, 17:27:49 UTC
ff75b75 [maven-release-plugin] prepare release 1.5.0-beta.6 05 September 2018, 17:27:44 UTC
b96bec5 Description update to include warning #1717 (#1791) 05 September 2018, 17:23:39 UTC
2351c8a Fix for sorting and filtering (#1785) * Fix for sorting and filtering * Update WorkflowIT.java 04 September 2018, 14:06:34 UTC
fa522b1 [maven-release-plugin] prepare for next development iteration 31 August 2018, 18:44:12 UTC
d8c21e8 [maven-release-plugin] prepare release 1.5.0-beta.5 31 August 2018, 18:44:02 UTC
f647b47 Feature/secure more (#1782) * Starring unpublished entries not allowed * Describe metadata in swagger * Transfer over tests 31 August 2018, 17:36:14 UTC
298c9af Feature/more refresh fixes (#1781) * Need more ordering for #1777 * Add fix and test for #1779 30 August 2018, 15:14:26 UTC
a1733dc 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 [maven-release-plugin] prepare for next development iteration 28 August 2018, 14:10:42 UTC
96f670a [maven-release-plugin] prepare release 1.5.0-beta.4 28 August 2018, 14:10:37 UTC
17ef8b7 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 Fix build (#1767) 27 August 2018, 17:21:13 UTC
4f6649b On self-destruct, delete user's workflows and tools (#1766) #1697 27 August 2018, 16:00:30 UTC
649cad4 Feature/1240/auto convert yaml (#1760) * Handle yaml files * Add test * Revert Help change (#1255) 24 August 2018, 19:38:50 UTC
83bcc83 Feature/regression (#1757) * Cleanup * Reactivate regression tests 24 August 2018, 18:45:04 UTC
d32585d 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 [maven-release-plugin] prepare for next development iteration 22 August 2018, 19:23:37 UTC
b90ecb6 [maven-release-plugin] prepare release 1.5.0-beta.3 22 August 2018, 19:23:31 UTC
0e9ca02 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 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 Add dates to workflows at create time (#1752) 22 August 2018, 17:40:59 UTC
77f0979 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 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 Feature/1698/tests (#1736) * initial tests * Refactor * PR changes * PR changes * More assertion 21 August 2018, 15:29:58 UTC
e4cf310 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 [maven-release-plugin] prepare for next development iteration 20 August 2018, 15:21:28 UTC
6aecc64 [maven-release-plugin] prepare release 1.5.0-beta.2 20 August 2018, 15:21:23 UTC
071fa54 Missing annotation for dag and tools (#1730) * Missing annotation * Fix permissions checking for test parameter files 20 August 2018, 15:18:19 UTC
fd6f7d7 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 [maven-release-plugin] prepare for next development iteration 17 August 2018, 18:38:24 UTC
a602ec4 [maven-release-plugin] prepare release 1.5.0-beta.1 17 August 2018, 18:38:18 UTC
2a2e545 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 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 Feature/duplicate hosted entry error (#1722) * ensure that users cannot add hosted entries with duplciate paths 16 August 2018, 20:39:46 UTC
bfa07b4 Manually suppress jersey logging for zip download (#1715) 16 August 2018, 14:10:23 UTC
7a74eb9 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 Login message (#1716) 15 August 2018, 15:17:14 UTC
5bd725e 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 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 [maven-release-plugin] prepare for next development iteration 13 August 2018, 21:26:28 UTC
1b92339 [maven-release-plugin] prepare release 1.5.0-beta.0 13 August 2018, 21:26:23 UTC
bbf51ea Remove orphan query 13 August 2018, 21:23:09 UTC
fe20a5a Not sure why this is in this branch 13 August 2018, 21:23:09 UTC
3235b48 Fix self-destruct DAO 13 August 2018, 21:23:09 UTC
ec0ddaa Laggard cleanup for TRS changes 13 August 2018, 21:23:09 UTC
446785c Feature/nextflow name conversion (#1702) * changed from nextflow to nfl, fixed issue 1662 13 August 2018, 19:51:03 UTC
a83e107 [maven-release-plugin] prepare for next development iteration 10 August 2018, 20:37:26 UTC
67a612c [maven-release-plugin] prepare release 1.5.0-alpha.10 10 August 2018, 20:37:21 UTC
76bd56d 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 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 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 Added an endpoint to check if a user with a given name exists (#1692) 08 August 2018, 18:42:28 UTC
d92cc5c 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 Replace all (#1686) * Replace all * Fix * Removed unused imports * Revert TRS change 07 August 2018, 18:44:21 UTC
bc4ad8a [maven-release-plugin] prepare for next development iteration 03 August 2018, 20:12:19 UTC
734228b [maven-release-plugin] prepare release 1.5.0-alpha.9 03 August 2018, 20:12:14 UTC
dbfc122 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 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 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 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 Elaborate on error messages (#1675) 02 August 2018, 14:31:06 UTC
ea3bb6d 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 Fixup path oddity for zip files (#1672) * Fixup path oddity for zip files 02 August 2018, 14:02:35 UTC
e24a5e5 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
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