https://github.com/ga4gh/dockstore

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Revision Author Date Message Commit Date
1b54374 [maven-release-plugin] prepare release 1.8.0-beta.5 09 January 2020, 16:38:55 UTC
72d2031 Cleanup 09 January 2020, 16:35:51 UTC
79e792d Fix up 08 January 2020, 22:51:36 UTC
f883731 Will need to test with CLI and UI2 08 January 2020, 22:48:06 UTC
dbb6e77 Feature/3045/recent events (#3096) * Add recent events related to starred entries 08 January 2020, 21:09:28 UTC
8e14672 removed HIGH priority; replaced with CRITICAL (#3110) 08 January 2020, 17:11:10 UTC
af50832 organisation accordion is now case senstitive (#3111) 07 January 2020, 19:28:38 UTC
8ec7662 Feature/3091/broken path (#3108) * Fix for null collection * Add test 07 January 2020, 17:50:44 UTC
9a4a06e Feature/3084/my entries db dates (#3103) * migration for last db update/create date to rational dates * db create and update for entry and versions are not nullable 07 January 2020, 16:07:33 UTC
8067f8d Feature/organisation open api (#3106) Added openapi3 annotations for organisation endpoints 07 January 2020, 13:57:59 UTC
132a68a Update 06 January 2020, 19:52:38 UTC
62e165e [maven-release-plugin] prepare for next development iteration 06 January 2020, 19:52:38 UTC
1dfa377 [maven-release-plugin] prepare release 1.8.0-beta.4 06 January 2020, 19:52:38 UTC
0a2e8c9 Take 2 06 January 2020, 19:52:38 UTC
78ffdf7 [maven-release-plugin] prepare for next development iteration 06 January 2020, 19:52:38 UTC
9153f69 [maven-release-plugin] prepare release 1.8.0-beta.3 06 January 2020, 19:52:38 UTC
fc6d6b5 Fix release process 06 January 2020, 19:52:38 UTC
fc9c38d Don't update on hosted workflow creation (#3105) 06 January 2020, 16:29:40 UTC
e754e0b Fix Docker image not building on Quay (#3098) 05 January 2020, 21:22:56 UTC
b7b0c5d [maven-release-plugin] prepare for next development iteration 03 January 2020, 20:37:12 UTC
4d7c92b [maven-release-plugin] prepare release 1.8.0-beta.2 03 January 2020, 20:37:06 UTC
ca232e0 Need newer swagger stuff? 03 January 2020, 20:34:02 UTC
66409fe [maven-release-plugin] prepare for next development iteration 03 January 2020, 20:11:48 UTC
c9a361e [maven-release-plugin] prepare release 1.8.0-beta.1 03 January 2020, 20:11:42 UTC
6af11d5 Feature/refresh all exception (#3102) * better error handling and message for refresh all 03 January 2020, 19:55:19 UTC
66aa5d2 [maven-release-plugin] prepare for next development iteration 02 January 2020, 16:45:48 UTC
0cab7ed [maven-release-plugin] prepare release 1.8.0-beta.0 02 January 2020, 16:45:41 UTC
df9cd81 Feature/seab 563/notifications backend (#2986) * four endpoints working * added integration tests * update null check * tests passing * removed unused import * added get/set for db dates * 401 status code * re-base and update ymls Co-authored-by: Louise Cabansay <lcabansa@ucsc.edu> 02 January 2020, 03:36:37 UTC
c99f3f2 Create workflow version aliases for zenodo related identifiers (#3087) Create workflow version aliases for zenodo related identifiers 20 December 2019, 22:23:45 UTC
6f08669 Ugly workaround for unit test failure on Travis (#3095) 20 December 2019, 21:09:10 UTC
8c991e3 Recursive Local Imports (#3060) 20 December 2019, 16:21:19 UTC
8dd74a7 gitlab checksums (#3053) Grab checksum from gitlab 19 December 2019, 21:07:03 UTC
71165e9 Add Dockerfile to web service (#3085) * Add Dockerfile to web service #3065 A small step towards continuous deploys, where we can get pre-built web service images from quay.io. Took dockstore/compose_setup/templates/Dockerfile_webservice.template and modified to make this file, with the main difference being that the webservice JAR is built instead of being pulled from OICR artifactory. Arguably shouldn't have dockerize waiting on postgres in here; OTOH the web service is useless without Postgres container. Also there was a comment about not hard-coding the dockstore_logs directory, but I left it hard-coded. We can revisit when we make the corresponding compose_setup changes. I have created https://quay.io/repository/dockstore-testing/dockstore-webservice and it images have been made against this branch. 19 December 2019, 17:47:12 UTC
19562e9 Allow only one simultaneous invocation of Nextflow (#3092) * Allow only one simultaneous invocation of Nextflow We run Nextflow JAR in a new VM. If multiple requests come in simultaneously, this will lead to a big slowdown in server responsiveness. * Fix checkstyle violations * Log some more stuff just in case. 19 December 2019, 16:53:48 UTC
d82382b [maven-release-plugin] prepare for next development iteration 19 December 2019, 03:14:41 UTC
cf17cab [maven-release-plugin] prepare release 1.8.0-alpha.3 19 December 2019, 03:14:41 UTC
d5bbca2 fix migration from prod 19 December 2019, 03:14:41 UTC
c97f2ad Has 3.6.7 python disappeared? 19 December 2019, 03:14:41 UTC
05eba26 Feature/stub migration (#3056) * delete all stub workflows and associated content 09 December 2019, 23:13:36 UTC
5d25197 Recent Entries Pretty Path (#3061) * return a pretty path for display on UI 06 December 2019, 23:36:20 UTC
6ecd967 Remove old verification endpoints (#3040) * Remove old verification endpoints * Remove unused test * Update openapi 05 December 2019, 17:18:51 UTC
68ba7bf Fix/3008/avatar url length (#3043) (#3057) * Migrate to unlimited length avatarUrl 05 December 2019, 15:20:42 UTC
99fced2 Remove deprecated test (#3048) * Remove deprecated test * fix imports 05 December 2019, 15:16:55 UTC
b002f5e Feature/2957/version metadata (#3024) * Initial get README implementation * Add some tests * Add description source, add version metadata * JsonIgnore default version * Set default version * Enhance test, update default version automatically * Add descriptor source 05 December 2019, 15:11:47 UTC
a3a980a get dockerhub checksum (#3039) dockerhub checksums 03 December 2019, 16:36:03 UTC
d81547d [maven-release-plugin] prepare for next development iteration 02 December 2019, 19:31:32 UTC
414d8b8 [maven-release-plugin] prepare release 1.8.0-alpha.2 02 December 2019, 19:31:25 UTC
c663750 Deprecate unstar, modify star to become restful (#3041) 29 November 2019, 16:58:36 UTC
9da4e46 Feature/migrate cli tests (#3038) Removed some tests that were CLI focused, converted many tests from CLI to API 28 November 2019, 16:28:23 UTC
c28d772 handle null case for get entries and get orgs (#3033) * handle null case for get entries and get orgs 28 November 2019, 14:10:55 UTC
afbbc24 Support workflow version aliases (#3005) Add alias support for workflow versions Add new workflow version endpoints for aliases Add integration test for workflow version aliases 22 November 2019, 21:22:57 UTC
fa08cb2 add featured content to webervice config (#3028) * add featured content to webervice config 21 November 2019, 19:32:23 UTC
9f726ad removed client calls from workflowIT and generalIT (#3030) Converted some tests that use CLI to use the API. Removed other tests which only tested CLI functions (these were moved to the CLI repo) 21 November 2019, 16:10:29 UTC
95737f7 sort versions by last modified date (#3027) 19 November 2019, 13:53:05 UTC
838b453 Feature/2254/seperate elasticsearch tests (#3025) * Restart elasticsearch between tests, move tests to IT 18 November 2019, 21:27:22 UTC
84bb6f6 Feature/2918/hosted tool provider (#3026) * fix for tool hosted git url * test that hosted tool have git url set 18 November 2019, 18:01:27 UTC
6ae0c39 Feature/2871/trs hidden versions (#3023) * Show hidden version in TRS when authenticated 18 November 2019, 14:56:32 UTC
ba17b9a Log exception when parsing WDL (#3016) #3015 Created a WdlBridge companion object so that a static logger can be used both in WdlBridge and WdlBridgeShutDown. Also had it use a class for the logger instead of a string, with a class being the way we do it elsewhere in the codebase. 08 November 2019, 21:06:46 UTC
c6172de Harvest Checksums from Quay (#3010) harvest checksums from Quay 08 November 2019, 16:57:11 UTC
9af8955 Use RSS cache (#3004) * Use RSS cache * Invalidate cache for updates too 07 November 2019, 16:26:19 UTC
0636822 Feature/fix circle ci (#3003) * Remove unused args * Use environment-wide JAVA_TOOL_OPTIONS to Xmx2g 01 November 2019, 17:01:59 UTC
a7cd7f7 Release/1.8.0 alpha.1 (#3002) * [maven-release-plugin] prepare release 1.8.0-alpha.1 * [maven-release-plugin] prepare for next development iteration * update swagger 01 November 2019, 12:38:23 UTC
560def6 Feature/homepage backend entries and orgs (#2995) * add endpoint for homepage entries and organisations * add test for homepage endpoints 31 October 2019, 15:40:00 UTC
68e960a Jackson updates (#2998) 30 October 2019, 19:39:03 UTC
bc91e17 prep DB for docker checksums (tools and workflows) (#2981) Add image table and store its checksums as a string in the database 30 October 2019, 15:53:10 UTC
7d14bdd RSS Endpoint Optimization (#2984) * Initial performance optimization for RSS endpoint * Simplify sitemap, remove sitemap service code * Fix test from previous PR 29 October 2019, 16:30:14 UTC
33e1f07 Feature/2761/null alias (#2979) * ntp * Eager load selected endpoints * Add assertion for alias 25 October 2019, 15:08:07 UTC
1242078 Feature/2933/cache sitemap (#2983) * Cache Sitemap endpoint * Use PublicStateManager * Change public state manager to always have listeners 25 October 2019, 13:41:15 UTC
234b511 Validate an alias before using it when creating a DOI (#2961) 24 October 2019, 00:28:39 UTC
d92129e Release/1.8.0 alpha.0 (#2980) * [maven-release-plugin] prepare release 1.8.0-alpha.0 * [maven-release-plugin] prepare for next development iteration * added swagger 22 October 2019, 14:47:29 UTC
95c3c7b Feature/get org repos return object (#2976) * get repos for org now returns objects 21 October 2019, 17:14:54 UTC
423cf22 Environment variable support for commands (#2975) * Environment variable support for commands #2971 Allow additional environment variables to be specified when running external commands. Commands will still use the "default" environment as a starting point; the variables specified will either be new or overrides. When running shell commands directly, need to call parse.setSubstitutionMap(additionalEnvironment) to get substitution to happen; 18 October 2019, 20:17:42 UTC
73e9844 Don't grab entire entity for sitemap performance (#2972) * Don't grab entire entity for sitemap 18 October 2019, 19:58:22 UTC
f54b31a use getTopicId instead of getId for generated discourse topics (#2936) 17 October 2019, 20:42:15 UTC
9afa513 Setup framework to let people work on caching (#2958) * Setup framework to let people work on caching * Hook up more resources (should be singleton) * PR feedback and singleton 16 October 2019, 21:04:44 UTC
e8501ec Fix WDL import issues (#2941) #2941 There were two problems: In WDLHandler.processImports, there is map of files that have been processed so that we don't process the same file more than once. The map key was just the filename, so if the same filename exists in more than one directory, the code would only process the first instance of the filename. Once getting past that, there were issues resolving imports, particularly if a WDL file imported from a sub-directory relatively imported more WDL from the same sub-directory. For the first issue, the key of the map is now the absolute path, so all files will get processed. The CWL code still works/expects a map with just the filename, so I changed the LanguageHandlerInterface.getContentto take a Set<SourceFile> instead of the Map<String, String>; that way each language implementation can internally construct their own Map for their needs. For the second issue, MapResolver now has a string to resolve imports relative to. Other notes * I committed the files from the workflow directly to the repo. It's a big one, but it might be good for other tests, and it simplifies the testing. * One test started to fail with these changes, DAGWorkflowTestIT.testComplexImportWdlWorkflow. However, running WOMTool validate standalone against the workflow also fails, so I think this is the correct behavior, and I updated the test to expect a failure. * There is a circular dependency with the CLI. Some tests are using the CLI which uses WDLBridge, which is in this project. Had to leave some old method signatures in there for the tests to run. * Needed to make SoruceCodeRepoInterface.getCommitId protected in order to have an implementation in the tests. * Also removed BridgeHelper.java, which isn't being used anywhere. * Removal of BridgeHelper means commons-validator no longer needed * Builds often failing on WDLHandlerTest or NFLParseTest; separate them out into their block of tests. * Using <argLine>-XX:+UseContainerSupport</argLine> to run the memory intensive tests caused NFLParseTest to fail, presumably because there wasn't enough memory to launch another JVM. Move it back into the regular unit tests. 14 October 2019, 17:12:10 UTC
4692611 Add row level security policy to join table (#2954) #2849 The table version_sourcefiles is a join table for the sourcefile table and the workflowversion/tag tables. If version is frozen, don't allow modifications -- no adding of additional source files, deletion nor modification of existing ones. Part of the ticket was to remove the application guards once database protection was implemented, but I decided against that -- Hibernate throws a 500 exception in that case. We would need to catch that exception and throw our own exception. The problem is the exception is thrown after the return statement code in the Java code for the resource endpoint -- the error happens because the @UnitOfWork annotation causes Hibernate to attempt to commit the transaction. We would have to remove the annotation, manually start the transaction and commit it. Which is doable, but doesn't seem like it would offer much over the current application guards. 11 October 2019, 16:24:27 UTC
89a0acd Feature/backend for workflow wizard (#2951) * endpoints for new workflow registration wizard 10 October 2019, 19:18:24 UTC
61e819e Fix adding aliases so that they do not overwrite existing aliases (#2948) Fix code from overwriting aliases Change add alias function name and fail for duplicated aliases Add tests for add alias that prevents duplicated and no delete Change names to reflect POST instead of PUT 09 October 2019, 21:40:46 UTC
c500c0e swagger-ui update (#2953) 09 October 2019, 19:53:32 UTC
6e212fa Feature/clean dag (#2940) * Remove edges that have undefined nodes 08 October 2019, 19:54:58 UTC
ccd28a8 Support saving the Zenodo concept DOI (#2926) Add support for saving and displaying the Zenodo concept DOI (DOI associated with the whole workflow) * add DB additions for concept DOI * add function for extracting doi from doi url * add test for doiUrl to doi * add 1.8.0 migration to test db * add negative test * add new migration version 04 October 2019, 20:21:29 UTC
4055588 remove checkstyle exemptions (#2924) 24 September 2019, 19:19:11 UTC
b7f63cd Remove dockstore-client and local launch tests (#2892) * moving toil tests to dockstore-cli if anything * simplifying profiles and associated tests in travis * moving out tests that are mostly about running workflows and tools 24 September 2019, 19:18:56 UTC
2b200db Feature/checkstyle expand (#2920) * Cut down on LGTM alerts * Failing openapi3 stability, we can make it smaller * Generic problem with java 11.0.2? https://bugs.openjdk.java.net/browse/JDK-8203195 * Expand testing to dockstore-integration-testing 23 September 2019, 18:09:29 UTC
cf43652 checkstyle upgrades in prep for expansion to tests (#2909) * checkstyle upgrades in prep for expansion to tests 20 September 2019, 20:48:07 UTC
214720f Merge tag '1.7.0' into develop [maven-release-plugin] copy for tag 1.7.0 20 September 2019, 20:13:50 UTC
75b9e0e [maven-release-plugin] prepare release 1.7.0 20 September 2019, 19:20:40 UTC
c71f1d7 Was blocking out syntax errors by accident (#2919) * was blocking out syntax errors by accident 20 September 2019, 17:39:44 UTC
5b0d9f0 synk guided updates (#2916) 20 September 2019, 16:38:48 UTC
34b28c9 Feature/dependency updates (#2914) * maven kongchen update * dropwizard update * swagger and openapi annotations update * Mockio fixes 19 September 2019, 16:10:34 UTC
0b65024 Rename swagger object (#2908) 18 September 2019, 17:50:05 UTC
e66d150 [maven-release-plugin] prepare for next development iteration 17 September 2019, 21:09:53 UTC
0166c6a [maven-release-plugin] prepare release 1.7.0-rc.3 17 September 2019, 21:09:47 UTC
6daba40 Feature/verification source and platform (#2887) * Fix for verified source and platform * Fix for metadata platform swap * Remove unused endpoints * Reorder positions for all swagger properties in version, tag, workflowversion 17 September 2019, 21:01:53 UTC
7f0783a Wombundle error handle (#2899) * handle error case 17 September 2019, 18:24:31 UTC
002e0a8 Oof fix2 (#2900) * fix * More laggard fix for descriptor type enum 17 September 2019, 17:04:12 UTC
5dbe735 [maven-release-plugin] prepare release 1.7.0-rc.2 16 September 2019, 19:36:40 UTC
0fed92d Known commands that break with 1.6.0 client (#2889) * Known commands that break with 1.6.0 client 16 September 2019, 19:36:40 UTC
1dbf21e Fix x-total-count for workflows/services (#2881) * Fix x-total-count for workflows/services 16 September 2019, 19:36:40 UTC
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