05e6759 | Denis Yuen | 03 January 2020, 21:01:28 UTC | [maven-release-plugin] prepare release 1.8.0-beta.4 | 03 January 2020, 21:01:28 UTC |
349d7c4 | Denis Yuen | 03 January 2020, 20:58:34 UTC | Take 2 | 03 January 2020, 20:58:34 UTC |
c43c4e4 | Denis Yuen | 03 January 2020, 20:53:46 UTC | [maven-release-plugin] prepare for next development iteration | 03 January 2020, 20:53:46 UTC |
1617e81 | Denis Yuen | 03 January 2020, 20:53:40 UTC | [maven-release-plugin] prepare release 1.8.0-beta.3 | 03 January 2020, 20:53:40 UTC |
09da77a | Denis Yuen | 03 January 2020, 20:50:01 UTC | Fix release process | 03 January 2020, 20:50:01 UTC |
b7b0c5d | Denis Yuen | 03 January 2020, 20:37:12 UTC | [maven-release-plugin] prepare for next development iteration | 03 January 2020, 20:37:12 UTC |
4d7c92b | Denis Yuen | 03 January 2020, 20:37:06 UTC | [maven-release-plugin] prepare release 1.8.0-beta.2 | 03 January 2020, 20:37:06 UTC |
ca232e0 | Denis Yuen | 03 January 2020, 20:34:02 UTC | Need newer swagger stuff? | 03 January 2020, 20:34:02 UTC |
66409fe | Denis Yuen | 03 January 2020, 20:11:48 UTC | [maven-release-plugin] prepare for next development iteration | 03 January 2020, 20:11:48 UTC |
c9a361e | Denis Yuen | 03 January 2020, 20:11:42 UTC | [maven-release-plugin] prepare release 1.8.0-beta.1 | 03 January 2020, 20:11:42 UTC |
6af11d5 | Andrew Duncan | 03 January 2020, 19:55:19 UTC | Feature/refresh all exception (#3102) * better error handling and message for refresh all | 03 January 2020, 19:55:19 UTC |
66aa5d2 | Denis Yuen | 02 January 2020, 16:45:48 UTC | [maven-release-plugin] prepare for next development iteration | 02 January 2020, 16:45:48 UTC |
0cab7ed | Denis Yuen | 02 January 2020, 16:45:41 UTC | [maven-release-plugin] prepare release 1.8.0-beta.0 | 02 January 2020, 16:45:41 UTC |
df9cd81 | emlys | 02 January 2020, 03:36:37 UTC | 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 | Walter Shands | 20 December 2019, 22:23:45 UTC | 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 | Charles Overbeck | 20 December 2019, 21:09:10 UTC | Ugly workaround for unit test failure on Travis (#3095) | 20 December 2019, 21:09:10 UTC |
8c991e3 | Gary Luu | 20 December 2019, 16:21:19 UTC | Recursive Local Imports (#3060) | 20 December 2019, 16:21:19 UTC |
8dd74a7 | NatalieEO | 19 December 2019, 21:07:03 UTC | gitlab checksums (#3053) Grab checksum from gitlab | 19 December 2019, 21:07:03 UTC |
71165e9 | Charles Overbeck | 19 December 2019, 17:47:12 UTC | 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 | Charles Overbeck | 19 December 2019, 15:40:12 UTC | 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 | Denis Yuen | 18 December 2019, 16:32:23 UTC | [maven-release-plugin] prepare for next development iteration | 19 December 2019, 03:14:41 UTC |
cf17cab | Denis Yuen | 18 December 2019, 16:32:17 UTC | [maven-release-plugin] prepare release 1.8.0-alpha.3 | 19 December 2019, 03:14:41 UTC |
d5bbca2 | Denis Yuen | 17 December 2019, 20:36:24 UTC | fix migration from prod | 19 December 2019, 03:14:41 UTC |
c97f2ad | Denis Yuen | 17 December 2019, 17:26:12 UTC | Has 3.6.7 python disappeared? | 19 December 2019, 03:14:41 UTC |
05eba26 | Andrew Duncan | 09 December 2019, 23:13:36 UTC | Feature/stub migration (#3056) * delete all stub workflows and associated content | 09 December 2019, 23:13:36 UTC |
5d25197 | Andrew Duncan | 06 December 2019, 23:36:20 UTC | Recent Entries Pretty Path (#3061) * return a pretty path for display on UI | 06 December 2019, 23:36:20 UTC |
6ecd967 | Gary Luu | 05 December 2019, 17:18:51 UTC | Remove old verification endpoints (#3040) * Remove old verification endpoints * Remove unused test * Update openapi | 05 December 2019, 17:18:51 UTC |
68ba7bf | Denis Yuen | 05 December 2019, 15:20:42 UTC | Fix/3008/avatar url length (#3043) (#3057) * Migrate to unlimited length avatarUrl | 05 December 2019, 15:20:42 UTC |
99fced2 | Gary Luu | 05 December 2019, 15:16:55 UTC | Remove deprecated test (#3048) * Remove deprecated test * fix imports | 05 December 2019, 15:16:55 UTC |
b002f5e | Gary Luu | 05 December 2019, 15:11:47 UTC | 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 | NatalieEO | 03 December 2019, 16:36:03 UTC | get dockerhub checksum (#3039) dockerhub checksums | 03 December 2019, 16:36:03 UTC |
d81547d | Denis Yuen | 02 December 2019, 19:31:32 UTC | [maven-release-plugin] prepare for next development iteration | 02 December 2019, 19:31:32 UTC |
414d8b8 | Denis Yuen | 02 December 2019, 19:31:25 UTC | [maven-release-plugin] prepare release 1.8.0-alpha.2 | 02 December 2019, 19:31:25 UTC |
c663750 | Gary Luu | 29 November 2019, 16:58:36 UTC | Deprecate unstar, modify star to become restful (#3041) | 29 November 2019, 16:58:36 UTC |
9da4e46 | Andrew Duncan | 28 November 2019, 16:28:23 UTC | 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 | Andrew Duncan | 28 November 2019, 14:10:55 UTC | 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 | Walter Shands | 22 November 2019, 21:22:57 UTC | 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 | Louise Cabansay | 21 November 2019, 19:32:23 UTC | add featured content to webervice config (#3028) * add featured content to webervice config | 21 November 2019, 19:32:23 UTC |
9f726ad | Andrew Duncan | 21 November 2019, 16:10:29 UTC | 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 | Andrew Duncan | 19 November 2019, 13:53:05 UTC | sort versions by last modified date (#3027) | 19 November 2019, 13:53:05 UTC |
838b453 | Gary Luu | 18 November 2019, 21:27:22 UTC | Feature/2254/seperate elasticsearch tests (#3025) * Restart elasticsearch between tests, move tests to IT | 18 November 2019, 21:27:22 UTC |
84bb6f6 | Andrew Duncan | 18 November 2019, 18:01:27 UTC | 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 | Gary Luu | 18 November 2019, 14:56:32 UTC | Feature/2871/trs hidden versions (#3023) * Show hidden version in TRS when authenticated | 18 November 2019, 14:56:32 UTC |
ba17b9a | Charles Overbeck | 08 November 2019, 21:06:46 UTC | 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 | NatalieEO | 08 November 2019, 16:57:11 UTC | Harvest Checksums from Quay (#3010) harvest checksums from Quay | 08 November 2019, 16:57:11 UTC |
9af8955 | Gary Luu | 07 November 2019, 16:26:19 UTC | Use RSS cache (#3004) * Use RSS cache * Invalidate cache for updates too | 07 November 2019, 16:26:19 UTC |
0636822 | Gary Luu | 01 November 2019, 17:01:59 UTC | Feature/fix circle ci (#3003) * Remove unused args * Use environment-wide JAVA_TOOL_OPTIONS to Xmx2g | 01 November 2019, 17:01:59 UTC |
a7cd7f7 | Andrew Duncan | 01 November 2019, 12:38:23 UTC | 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 | Andrew Duncan | 31 October 2019, 15:40:00 UTC | 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 | Denis Yuen | 30 October 2019, 19:39:03 UTC | Jackson updates (#2998) | 30 October 2019, 19:39:03 UTC |
bc91e17 | NatalieEO | 30 October 2019, 15:53:10 UTC | 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 | Gary Luu | 29 October 2019, 16:30:14 UTC | 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 | Gary Luu | 25 October 2019, 15:08:07 UTC | Feature/2761/null alias (#2979) * ntp * Eager load selected endpoints * Add assertion for alias | 25 October 2019, 15:08:07 UTC |
1242078 | Gary Luu | 25 October 2019, 13:41:15 UTC | 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 | Walter Shands | 24 October 2019, 00:28:39 UTC | Validate an alias before using it when creating a DOI (#2961) | 24 October 2019, 00:28:39 UTC |
d92129e | Andrew Duncan | 22 October 2019, 14:47:29 UTC | 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 | Andrew Duncan | 21 October 2019, 17:14:54 UTC | Feature/get org repos return object (#2976) * get repos for org now returns objects | 21 October 2019, 17:14:54 UTC |
423cf22 | Charles Overbeck | 18 October 2019, 20:17:42 UTC | 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 | Gary Luu | 18 October 2019, 19:58:22 UTC | Don't grab entire entity for sitemap performance (#2972) * Don't grab entire entity for sitemap | 18 October 2019, 19:58:22 UTC |
f54b31a | Andrew Duncan | 02 October 2019, 16:58:25 UTC | use getTopicId instead of getId for generated discourse topics (#2936) | 17 October 2019, 20:42:15 UTC |
9afa513 | Denis Yuen | 16 October 2019, 21:04:44 UTC | 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 | Charles Overbeck | 14 October 2019, 17:12:10 UTC | 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 | Charles Overbeck | 11 October 2019, 16:24:27 UTC | 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 | Andrew Duncan | 10 October 2019, 19:18:24 UTC | Feature/backend for workflow wizard (#2951) * endpoints for new workflow registration wizard | 10 October 2019, 19:18:24 UTC |
61e819e | Walter Shands | 09 October 2019, 21:40:46 UTC | 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 | Denis Yuen | 09 October 2019, 19:53:32 UTC | swagger-ui update (#2953) | 09 October 2019, 19:53:32 UTC |
6e212fa | Gary Luu | 08 October 2019, 19:54:58 UTC | Feature/clean dag (#2940) * Remove edges that have undefined nodes | 08 October 2019, 19:54:58 UTC |
ccd28a8 | Walter Shands | 04 October 2019, 20:21:29 UTC | 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 | Denis Yuen | 24 September 2019, 19:19:11 UTC | remove checkstyle exemptions (#2924) | 24 September 2019, 19:19:11 UTC |
b7f63cd | Denis Yuen | 24 September 2019, 19:18:56 UTC | 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 | Denis Yuen | 23 September 2019, 18:09:29 UTC | 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 | Denis Yuen | 20 September 2019, 20:48:07 UTC | 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 | Denis Yuen | 20 September 2019, 20:13:50 UTC | Merge tag '1.7.0' into develop [maven-release-plugin] copy for tag 1.7.0 | 20 September 2019, 20:13:50 UTC |
75b9e0e | Denis Yuen | 20 September 2019, 19:20:40 UTC | [maven-release-plugin] prepare release 1.7.0 | 20 September 2019, 19:20:40 UTC |
c71f1d7 | Andrew Duncan | 20 September 2019, 17:39:44 UTC | Was blocking out syntax errors by accident (#2919) * was blocking out syntax errors by accident | 20 September 2019, 17:39:44 UTC |
5b0d9f0 | Denis Yuen | 20 September 2019, 16:38:48 UTC | synk guided updates (#2916) | 20 September 2019, 16:38:48 UTC |
34b28c9 | Denis Yuen | 19 September 2019, 16:10:34 UTC | Feature/dependency updates (#2914) * maven kongchen update * dropwizard update * swagger and openapi annotations update * Mockio fixes | 19 September 2019, 16:10:34 UTC |
0b65024 | Gary Luu | 18 September 2019, 17:50:05 UTC | Rename swagger object (#2908) | 18 September 2019, 17:50:05 UTC |
e66d150 | Denis Yuen | 17 September 2019, 21:09:53 UTC | [maven-release-plugin] prepare for next development iteration | 17 September 2019, 21:09:53 UTC |
0166c6a | Denis Yuen | 17 September 2019, 21:09:47 UTC | [maven-release-plugin] prepare release 1.7.0-rc.3 | 17 September 2019, 21:09:47 UTC |
6daba40 | Gary Luu | 17 September 2019, 21:01:53 UTC | 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 | Andrew Duncan | 17 September 2019, 18:24:31 UTC | Wombundle error handle (#2899) * handle error case | 17 September 2019, 18:24:31 UTC |
002e0a8 | Denis Yuen | 17 September 2019, 17:04:12 UTC | Oof fix2 (#2900) * fix * More laggard fix for descriptor type enum | 17 September 2019, 17:04:12 UTC |
5dbe735 | Denis Yuen | 13 September 2019, 21:02:27 UTC | [maven-release-plugin] prepare release 1.7.0-rc.2 | 16 September 2019, 19:36:40 UTC |
0fed92d | Denis Yuen | 13 September 2019, 17:48:26 UTC | 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 | Gary Luu | 12 September 2019, 19:42:00 UTC | Fix x-total-count for workflows/services (#2881) * Fix x-total-count for workflows/services | 16 September 2019, 19:36:40 UTC |
57df1bb | Denis Yuen | 12 September 2019, 15:54:07 UTC | Regression switches from 1.4.5 to 1.6.0 | 16 September 2019, 19:36:40 UTC |
d53cf4d | Denis Yuen | 12 September 2019, 15:36:22 UTC | Toil tests too messed up by Python3 | 16 September 2019, 19:36:40 UTC |
488dbcb | Denis Yuen | 16 September 2019, 18:54:31 UTC | fix (#2896) | 16 September 2019, 18:54:31 UTC |
926e82a | Gary Luu | 16 September 2019, 14:46:35 UTC | Feature/2871/hidden version get test parameter file (#2888) * Don't filter hidden versions if isUser | 16 September 2019, 14:46:35 UTC |
a673569 | Denis Yuen | 13 September 2019, 21:02:33 UTC | [maven-release-plugin] prepare for next development iteration | 13 September 2019, 21:02:33 UTC |
1c47eca | Denis Yuen | 13 September 2019, 21:02:27 UTC | [maven-release-plugin] prepare release 1.7.0-rc.2 | 13 September 2019, 21:02:27 UTC |
5cc6d62 | Denis Yuen | 13 September 2019, 17:48:26 UTC | Known commands that break with 1.6.0 client (#2889) * Known commands that break with 1.6.0 client | 13 September 2019, 17:48:26 UTC |
aa00445 | Gary Luu | 12 September 2019, 19:42:00 UTC | Fix x-total-count for workflows/services (#2881) * Fix x-total-count for workflows/services | 12 September 2019, 19:42:00 UTC |
d031e4d | Andrew Duncan | 12 September 2019, 19:37:53 UTC | add rtd badge to readme (#2885) * add rtd badge to readme * fix gitter link | 12 September 2019, 19:37:53 UTC |
37e5662 | Gary Luu | 12 September 2019, 17:27:35 UTC | Feature/2871/hidden version get test parameter file (#2879) * Don't filter hidden versions if isUser * Add test | 12 September 2019, 17:27:35 UTC |
73245ec | Denis Yuen | 12 September 2019, 15:54:07 UTC | Regression switches from 1.4.5 to 1.6.0 | 12 September 2019, 15:54:07 UTC |
be866d3 | Denis Yuen | 12 September 2019, 15:36:22 UTC | Toil tests too messed up by Python3 | 12 September 2019, 15:36:22 UTC |
239a616 | Denis Yuen | 12 September 2019, 14:23:56 UTC | iterate version numbers for 1.8.0 | 12 September 2019, 14:23:56 UTC |
840cf87 | Denis Yuen | 11 September 2019, 21:49:06 UTC | update secret archive | 11 September 2019, 21:50:05 UTC |