https://github.com/ga4gh/dockstore

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Revision Author Date Message Commit Date
0c57566 [maven-release-plugin] prepare release 1.9.2 14 October 2020, 23:27:44 UTC
5fc0963 Fix/seab 1697/get tool by id fix (#3827) * Handle nulls * Add checker id constraint * Add migration 25 September 2020, 21:54:50 UTC
5caaad2 fixDagAndTools (#3794) * For #3349 handle import/include with and without a prepending $. * For #3797 Avoid NPEs by using Optional. * Had to fix some tests since more steps are detected now. 23 September 2020, 17:58:51 UTC
aa49fb4 Cache GitHub app tokens for a little less time (#3782) https://ucsc-cgl.atlassian.net/browse/SEAB-1691 We are occassionaly seeing bad credentials errors for the GitHub token in the logs. This is a bit of a speculative fix, but I have seen similar problems in other environments of using a token that has expired. The speculation is: Token is good for one hour, we cache it for one hour. We fetch the token from the cache .5 seconds before it expires. Making the GitHub API calls takes more than .5 seconds; token is expired and call fails. 2 minutes buffer may seem overkill, but maybe the network is sluggish, the web service is bogged down, and a huge repo needs to be cloned. 02 September 2020, 22:04:07 UTC
d9cf464 bitbucket bug (#3779) #3568 don't try to read a sourcefile from bitbucket if its path is empty 02 September 2020, 17:30:17 UTC
01347ad Feature/seab 1675/pushtoquay (#3773) SEAB-1675 Build the Docker image on CircleCI, push to Quay. Quay builds were failing to build for reasons I couldn't figure out. So build on CircleCI, where we already have the JAR, and push to Quay. 01 September 2020, 16:28:12 UTC
56e4f63 .dockstore.yml in .github/ dir & Adding filters to .dockstore.yml (#3733) (#3769) * add filters to .dockstore.yml (WIP - needs tests) * add .github/.dockstore.yml as alternative .dockstore.yml path * tests for .dockstore.yml in .github/ & filters * fix misleading filters comment * filtering code for workflows/services abstracted into 1 function * remove leading slash from filters glob pathMatcher * remove leading ** from filters matching & use a git reference "template" * relocate filterGitReference() and negate boolean result * move function above inner class to fix checkstyle error * regex filters (surround with /) & unit test * separate tags and branches filters; broken WebHookIT test needs fixing * fixed integration tests: allow null filters, handle/log regex errors * fix unit test - regex error no longer fails * remove unused imports from unit tests * throw exception on invalid git reference * use UnsupportedOperationException for invalid git reference error * invalid glob/regex unit test, matcher catch UnsupportedOperation * close comment bracket 28 August 2020, 13:24:21 UTC
0204b00 update to admin, maintainer, and member organization user roles (#3762) * update to admin, maintainer, and member organization user roles #3742 27 August 2020, 16:35:18 UTC
4aa9536 1502 better date sort (#3753) * Pray * Use last modified only 27 August 2020, 13:01:03 UTC
37eede4 use getters for Tag compareTo() (#3702) (#3746) * use getters for Tag compareTo() * make name, reference, & lastBuilt private to be safe 14 August 2020, 19:06:46 UTC
3c57ff8 TRS tools endpoint - exclude null values for provided parameters (#3707) (#3745) * TRS tools endpoint - exclude null values for provided parameters * add relevant assertions to tool list test (last one used to fail) 14 August 2020, 16:31:11 UTC
4aa0701 Fix/seab 1502/lazy versions (#3732) * See what breaks * Fix some tests * Fix? * Fix * Revert weird removal * Increase size, add firstResult * Fix checkstyle * Add comment about pagination limit * Add versionName query parameter * Don't paginate unnecessary endpoints * Fix tests * Handle unknown version name * Move queries around, use named queries * Update openapi/swagger * Fix * Fix queries * One last namedQuery * Fix * PR changes * Use unique result * Change to long 13 August 2020, 23:08:46 UTC
57dc7a9 3487/smart refresh (#3720) * smart refresh for refresh workflow and refresh workflow version * default tests to soft refresh https://github.com/dockstore/dockstore/issues/3487 10 August 2020, 19:22:20 UTC
ad98c7d Merge branch 'hotfix/1.9.1' 06 August 2020, 15:13:41 UTC
6b11b9a autogen changes 06 August 2020, 15:13:29 UTC
1379065 [maven-release-plugin] prepare for next development iteration 06 August 2020, 15:06:28 UTC
ef25990 [maven-release-plugin] prepare release 1.9.1 06 August 2020, 15:06:20 UTC
1c23e99 Set batch size for associations (#3668) (#3700) * Set batch size for associations #2125 Instead of fetching each association row one-by-one, fetches them in batches. For example, if a entry has 10 versions, the 10 versions will be fetched in one SQL statement when batch size is >= 10. If batch size is not set, the 10 versions are fetched with 10 SQL statements. A lot more details on PR. 29 July 2020, 22:57:55 UTC
65d1d98 3687/lambda error message fix (#3696) * print out error message to lambda event for customwebapplicationexceptions * change to one liner 28 July 2020, 17:53:57 UTC
e8ea44b Hopefully less openapi.yaml changes 28 July 2020, 14:54:28 UTC
7d75576 Working example for cofest 28 July 2020, 14:54:28 UTC
ba23a29 Support Develop TRS (#3671) * Use another branch of TRS where Galaxy is GALAXY * Make use of new descriptor name * Update openapi * Use tagged version 28 July 2020, 14:54:28 UTC
41ddaf3 Support GALAXY subclass in .dockstore.yml (#3690) * Support GALAXY subclass in .dockstore.yml #3686 Continue to support GXFORMAT2 for backwards-compatiblity, and continue to expose GXFORMAT2 in the object for code that already relies on that. There is probably a more elegant solution with snakeyaml, but it wasn't immediately obvious, and this should work. 24 July 2020, 22:51:56 UTC
e41902f PullRobot reference in wrong place, add more tests (#3655) 10 July 2020, 20:59:37 UTC
f617f49 Fix/3619/add user to dockstore workflows performance (#3646) * Use existing optimized query * Only grab workflows without the user 08 July 2020, 14:40:16 UTC
1c481c3 Fix bad merge to master (#3625) LGTM check failing because it can't build the previous commit, which this PR fixes. 30 June 2020, 16:02:29 UTC
8222408 Merge branch 'release/1.9.0' 29 June 2020, 20:40:17 UTC
e5508d0 [maven-release-plugin] prepare for next development iteration 29 June 2020, 20:18:03 UTC
fba46c9 [maven-release-plugin] prepare release 1.9.0 29 June 2020, 20:17:54 UTC
9cb47b4 Fix discover workflows (#3621) #3486 findMyEntries is returning both workflows and services, so filter on BioWorkflows. Debated about whether to deeper changes for this, but instead created a followup issue, #3619. I don't know why Swagger/OpenAPI/third-party is so out of sync Seems coveralls if flaky and we need this for release, so merging 29 June 2020, 20:03:02 UTC
6fe6db9 [maven-release-plugin] prepare for next development iteration 24 June 2020, 18:41:30 UTC
15f8f68 [maven-release-plugin] prepare release 1.9.0-beta.2 24 June 2020, 18:41:23 UTC
29cc8c4 Feature/3035/requirements map error (#3587) * support for cwl requirements and hints as maps * added test for requirements https://github.com/dockstore/dockstore/issues/3035 24 June 2020, 17:45:17 UTC
fb13a51 added timeout to executeCommand utilities (#3548) added timeout to executeCommand utilities 24 June 2020, 17:03:00 UTC
5ae940e Feature/3540/quay swagger pull robot field (#3602) * Update pull_robot swagger 24 June 2020, 16:22:39 UTC
9ac55b9 Disable known CLI breakage (#3597) 22 June 2020, 21:50:06 UTC
2559d6b fix npe plus test (#3581) * fix plus test * Fix for npe 22 June 2020, 17:42:59 UTC
08ff191 [maven-release-plugin] prepare for next development iteration 18 June 2020, 15:30:53 UTC
06d2100 [maven-release-plugin] prepare release 1.9.0-beta.1 18 June 2020, 15:30:45 UTC
403aa9c Feature/3551/fix default version migration (#3554) 18 June 2020, 15:18:15 UTC
5a5ce29 Feature/3097/duplicate token registration (#3566) * properly catch error where a 3rd party account has already been connected https://github.com/dockstore/dockstore/issues/3097 17 June 2020, 14:36:17 UTC
cbedbd9 Feature/3572/catch http import exceptions (#3573) * prevent check for http recursive imports from throwing exception that kills refresh https://github.com/dockstore/dockstore/issues/3572 16 June 2020, 20:18:05 UTC
01e6ba1 Feature/3412/dockstoreyml metadata capture (#3567) * keep track of dockstore yml metadata * automatic code fix https://github.com/dockstore/dockstore/issues/3412 16 June 2020, 15:39:00 UTC
464a35e Feature/log readfile error log path (#3556) * include file name in log for io exception from readfile * improve the error message for the readFile call * some more improvements to logging * a few more logging updates * throw exception when cannot reach the repository on github * print exception as well 12 June 2020, 15:24:22 UTC
26e7001 feature/3406/add openapi lock to endpoint (#3547) * missing endpoint 11 June 2020, 23:30:24 UTC
39bc462 Feature/remove refreshorg (#3538) * tests now mostly use a combination of listing repos by organization membership and manual register to simulate what we used to do with refresh by org 11 June 2020, 20:34:31 UTC
d6e10d2 Don't allow curators and admins to login with Google (#3545) * Don't allow curators and admins to login with Google SEAB-1346 We enforce MFA for the dockstore GitHub org, and only make dockstore GitHub members eligible for being admins and curators. Not aware of a way to enforce MFA for a Google account, so disable logging in with Google if you are an admin or curator. 11 June 2020, 16:09:11 UTC
c12b916 Add additional tool deletion case (#3543) 10 June 2020, 15:07:28 UTC
653c2de Release/1.9.0 beta.0 (#3537) * [maven-release-plugin] prepare release 1.9.0-beta.0 * [maven-release-plugin] prepare for next development iteration * update swagger and openapi 09 June 2020, 15:57:46 UTC
0149fc2 switch to https://schema.org/version/latest/schema.rdf (#3526) Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com> 08 June 2020, 23:11:13 UTC
5bea225 Feature/fix tool date (#3535) * Fix tool date * Revert "fix hosted tool delete error (#3533)" This reverts commit 9514cd90bded8ab78c3dc4c24350a6ace715687c. * Use Apache instead instead of plain Java 08 June 2020, 17:19:28 UTC
9514cd9 fix hosted tool delete error (#3533) * use dbcreatetime for finding most recent version 08 June 2020, 13:57:19 UTC
83af273 Release/1.9.0 alpha.10 (#3532) * [maven-release-plugin] prepare release 1.9.0-alpha.10 * [maven-release-plugin] prepare for next development iteration * update swagger and openapi 05 June 2020, 19:42:25 UTC
b78abb8 lambda event organization column and date (#3529) * return date in json object; also split repository into organization and repository * fix migration 05 June 2020, 17:14:14 UTC
5c0b5d5 put lock on applicable openapi endpoints (#3512) * put lock on applicable openapi endpoints #3406 04 June 2020, 18:21:20 UTC
45959c0 Extra message for invalid repo (#3520) * Extra message for invalid repo * PR feedback 03 June 2020, 18:42:37 UTC
47be4cc Allow only one service in .dockstore.yml (#3515) * Allow only one service in .dockstore.yml #3460 Instead of array of services, only allow one. See issue for details. 03 June 2020, 16:20:56 UTC
22cf052 Fix typo in printed message in DockstoreYamlHelper (#3513) 02 June 2020, 23:30:30 UTC
3d73785 Merge 1.8.6 hotfix take3 (#3506) 02 June 2020, 19:22:27 UTC
15f3e6c Release/1.9.0 alpha.9 (#3511) * [maven-release-plugin] prepare release 1.9.0-alpha.9 * [maven-release-plugin] prepare for next development iteration 02 June 2020, 17:31:06 UTC
5e0deaa Feature/1360/test params not required (#3507) * test param file not required * add test for empty test param file https://github.com/dockstore/dockstore/issues/3466 01 June 2020, 13:47:38 UTC
30b8f38 Feature/3486/endpoint add user to workflows (#3491) * add endpoint for adding user to all workflows they should have access to https://github.com/dockstore/dockstore/issues/3486 29 May 2020, 20:00:17 UTC
53013f9 Feature/3449/set default version during refresh (#3498) * Add another test 29 May 2020, 17:43:53 UTC
cb794a5 Feature/3238/lambda error messages (#3479) * Store lambda events and make them accessible via API https://github.com/dockstore/dockstore/issues/3238 29 May 2020, 15:34:07 UTC
2df76fe Sourcefiles endpoint (#3482) sourcefiles endpoint 28 May 2020, 19:23:27 UTC
b025432 Merge branch 'hotfix/1.8.6' 28 May 2020, 15:41:49 UTC
4f32ff5 [maven-release-plugin] prepare for next development iteration 28 May 2020, 15:25:01 UTC
6632e5b [maven-release-plugin] prepare release 1.8.6 28 May 2020, 15:24:54 UTC
c2d5de0 Fix/keep old models (#3496) * Make compatible with CLI * Convert back to Workflow * Revert MyWorkflow swagger 27 May 2020, 17:30:25 UTC
6ca5b26 Fix/store jar on circle ci (#3497) * Store artifacts * change order of migrations in migrations.xml (#3375) Co-authored-by: Andrew Duncan <andrew.duncan@oicr.on.ca> 27 May 2020, 17:29:45 UTC
f9a9a1c Fix tool delete when events are present (#3494) 25 May 2020, 18:41:57 UTC
02a765d Bump commons-configuration2 from 2.2 to 2.7 (#3492) * Bump commons-configuration2 from 2.2 to 2.7 Bumps commons-configuration2 from 2.2 to 2.7. Signed-off-by: dependabot[bot] <support@github.com> * Update managed commons-text (might affect Cromwell) Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Denis Yuen <denis.yuen@oicr.on.ca> 25 May 2020, 18:41:28 UTC
e9a98e6 Feature/fix discourse api (#3471) * https://ucsc-cgl.atlassian.net/browse/SEAB-1135 * better error message for discourse * update discourse swagger 20 May 2020, 15:12:40 UTC
d22cc74 Fix/logged out collection entries (#3481) * Fix logged out entries * Prevent from ever happening again 20 May 2020, 00:33:12 UTC
d4a7b6e Lazy load event entities (#3478) 19 May 2020, 21:27:37 UTC
b86ec62 Feature/fixTravisPostgres (#3480) * Test * I believe! 19 May 2020, 18:57:19 UTC
e1277af Fix/seab 1132/collection entries (#3467) * Custom type for collection entries * Database optimization * Update openapi/swagger again 15 May 2020, 19:08:59 UTC
4fcc7ab Discourse fix (#3474) https://ucsc-cgl.atlassian.net/browse/SEAB-1135 Writing to Discourse now works again 14 May 2020, 14:32:15 UTC
7966409 Feature/3456/track git commit (#3470) https://github.com/dockstore/dockstore/issues/3456 Track commit ID for GitLab and Bitbucket workflows. 13 May 2020, 20:02:50 UTC
0a73eb3 bump to versions that contain license info (#3465) Co-authored-by: Denis Yuen <denis.yuen@oicr.on.ca> Co-authored-by: Andrew Duncan <andrew.duncan@oicr.on.ca> 12 May 2020, 16:02:56 UTC
b970f1b Simple sort when getting entries (#3463) 11 May 2020, 23:42:37 UTC
48807f0 Fix/3434/my workflows further optimization (#3462) * Initial payload optimization * Database optimization * Update swagger/openapi 11 May 2020, 19:59:04 UTC
a1b3e74 ref triple can be null, this is now accounted for (#3464) https://github.com/dockstore/dockstore/issues/3452 11 May 2020, 19:47:31 UTC
be75a74 successful descriptor validations will not have any messages (#3459) * successful validations will not have any messages * optimisation from Charles 08 May 2020, 12:52:43 UTC
d2f902c Feature/2955/delete test parameter file (#3427) * Throw error when file doesn't exist * Add tests 06 May 2020, 17:52:24 UTC
f494c55 Feature/3416/no service refresh (#3443) * do not allow service to be refreshed * test that you cannot refresh a service 05 May 2020, 13:01:02 UTC
96e3f40 Feature/3420/require file name (#3428) * Don't allow / as a name 01 May 2020, 23:13:46 UTC
be7c836 Enhance validation of dockstore.yml workflows (#3440) * add version even if primary descriptor is not present * record validation information for the .dockstore.yml 01 May 2020, 19:44:24 UTC
bc0fbaa Make Dockstore.YML relevant to Galaxy (#3436) 01 May 2020, 17:47:57 UTC
4f01e3f Merge tag '1.8.5' into develop [maven-release-plugin] copy for tag 1.8.5 30 April 2020, 17:50:43 UTC
1ff70a0 Merge branch 'hotfix/1.8.5' 30 April 2020, 17:48:32 UTC
51c22c8 [maven-release-plugin] prepare for next development iteration 30 April 2020, 17:23:07 UTC
ce3b465 [maven-release-plugin] prepare release 1.8.5 30 April 2020, 17:22:58 UTC
35d49e8 Json ignore collection entities, need a hibernate overrride (#3441) 30 April 2020, 17:11:55 UTC
b0a2bb2 Merge tag '1.8.4' into develop [maven-release-plugin] copy for tag 1.8.4 29 April 2020, 21:32:45 UTC
3f14674 Merge branch 'hotfix/1.8.4' 29 April 2020, 21:26:16 UTC
a2ec8dd [maven-release-plugin] prepare for next development iteration 29 April 2020, 19:01:38 UTC
3579ff9 [maven-release-plugin] prepare release 1.8.4 29 April 2020, 19:01:30 UTC
d70c95e Evict versions and users (#3435) 29 April 2020, 18:58:51 UTC
352364b [maven-release-plugin] prepare for next development iteration 28 April 2020, 23:16:36 UTC
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