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https://github.com/ga4gh/dockstore
05 April 2024, 22:18:50 UTC
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Revision Author Date Message Commit Date
977e3b8 Denis Yuen 22 February 2017, 17:22:28 UTC [maven-release-plugin] prepare release 1.1.4 22 February 2017, 17:22:28 UTC
3798bb7 Denis Yuen 22 February 2017, 17:20:47 UTC Fix webservice pom 22 February 2017, 17:20:47 UTC
1a0b5b0 Denis Yuen 22 February 2017, 16:49:12 UTC [maven-release-plugin] prepare for next development iteration 22 February 2017, 16:49:12 UTC
66a14f2 Denis Yuen 22 February 2017, 16:49:07 UTC [maven-release-plugin] prepare release 1.1.3 22 February 2017, 16:49:07 UTC
2f37a63 Denis Yuen 21 February 2017, 20:54:58 UTC Move to artifacts.oicr.on.ca 22 February 2017, 16:36:55 UTC
4f1248b Denis Yuen 15 February 2017, 16:58:59 UTC Improve performance for #586 Will implement user-configurable parameters when working on provisoning plugins next 15 February 2017, 16:58:59 UTC
ac5e507 Denis Yuen 10 February 2017, 18:47:48 UTC Mutate short name for icgc files #587 * needs to make it into file provisioning long-term 10 February 2017, 18:48:55 UTC
e914f52 Denis Yuen 10 February 2017, 17:13:53 UTC Feature/travis fix (#588) * Skip malformed client * Fix reference file location and mocking * Do some additional cleanup while at it 10 February 2017, 17:15:12 UTC
aa236ca Denis Yuen 10 February 2017, 16:18:55 UTC Iterate version number 10 February 2017, 16:18:55 UTC
8a952d5 Denis Yuen 17 January 2017, 15:42:04 UTC Merge branch 'hotfix/1.1.2' 17 January 2017, 15:42:04 UTC
3159061 Denis Yuen 16 January 2017, 22:04:13 UTC Fix test imports 16 January 2017, 22:04:13 UTC
ca647cb Denis Yuen 16 January 2017, 21:27:58 UTC Iterate version numbers 16 January 2017, 21:27:58 UTC
cc0f80f Denis Yuen 16 January 2017, 21:18:52 UTC Feature/file provisioning work (#574) * Working on file provisioning * Commit working fix for local file provision and tests 16 January 2017, 21:26:38 UTC
44e9a3f Denis Yuen 20 December 2016, 20:48:00 UTC Merge branch 'hotfix/1.1.1' 20 December 2016, 20:48:00 UTC
137c2fc Denis Yuen 20 December 2016, 20:03:20 UTC [maven-release-plugin] prepare for next development iteration 20 December 2016, 20:03:20 UTC
9b8dadb Denis Yuen 20 December 2016, 20:03:15 UTC [maven-release-plugin] prepare release 1.1.1 20 December 2016, 20:03:15 UTC
fb871d3 Denis Yuen 16 December 2016, 19:00:18 UTC Feature/secondary files output (#547) * Initial fix for secondary files provisioning on output * Add test for provison out * Update cwlavro to pass through output #533 16 December 2016, 19:01:03 UTC
6826667 Denis Yuen 16 December 2016, 15:44:53 UTC Set version number for hotfix branch 16 December 2016, 15:44:53 UTC
f6d7126 Denis Yuen 16 December 2016, 15:34:40 UTC Update README.md 16 December 2016, 15:43:10 UTC
738f4fd Denis Yuen 13 December 2016, 15:36:10 UTC Passive mode ftp? (#539) 16 December 2016, 15:42:48 UTC
cfa53b6 Denis Yuen 09 December 2016, 15:20:08 UTC Feature/java 9 experiment (#531) * Experiment with Java 9 on OpenStack * Is Maven 3.3.9 causing issues? * Looks like a rogue API return from GitHub kills builds 16 December 2016, 15:42:29 UTC
39d1efe Denis Yuen 08 December 2016, 16:29:27 UTC Feature/usability grab bag (#527) * Lock down existing behaviour with test * Reports from Travis-CI that Java 8 is setup properly * Move around messaging * Add ga4gh validation test 16 December 2016, 15:41:47 UTC
4e5c268 Denis Yuen 06 December 2016, 21:55:45 UTC Create CITATION 16 December 2016, 15:41:13 UTC
0e5fc64 Denis Yuen 16 December 2016, 15:33:19 UTC Merge tag '1.1' [maven-release-plugin] copy for tag 1.1 16 December 2016, 15:33:19 UTC
c038ede Denis Yuen 25 November 2016, 18:50:42 UTC [maven-release-plugin] prepare release 1.1 25 November 2016, 18:50:42 UTC
6635b54 Denis Yuen 24 November 2016, 21:42:23 UTC [maven-release-plugin] prepare for next development iteration 24 November 2016, 21:42:23 UTC
ea699a6 Denis Yuen 24 November 2016, 21:42:20 UTC [maven-release-plugin] prepare release 1.1-rc.2 24 November 2016, 21:42:20 UTC
7423dec Denis Yuen 24 November 2016, 21:39:15 UTC A couple of minor issues for #502 24 November 2016, 21:39:15 UTC
e0332de Denis Yuen 24 November 2016, 19:25:13 UTC Fix up test conflict 24 November 2016, 19:25:13 UTC
a847037 Denis Yuen 24 November 2016, 17:31:57 UTC Add partial test 24 November 2016, 17:31:57 UTC
2f6768a Denis Yuen 23 November 2016, 23:30:59 UTC Add hookup for ga4gh verified support, needs tests 23 November 2016, 23:30:59 UTC
20f7696 Denis Yuen 23 November 2016, 22:54:55 UTC Add missing help message 23 November 2016, 22:54:55 UTC
0eacbbd Andrew Duncan 23 November 2016, 19:58:59 UTC Update verified and dirtyBit to be false for existing entries 23 November 2016, 19:58:59 UTC
8299236 Denis Yuen 23 November 2016, 18:26:23 UTC [maven-release-plugin] prepare for next development iteration 23 November 2016, 18:26:23 UTC
e78a157 Denis Yuen 23 November 2016, 18:26:19 UTC [maven-release-plugin] prepare release 1.1-rc.1 23 November 2016, 18:26:19 UTC
90c982f Denis Yuen 23 November 2016, 18:24:45 UTC Iterate for release 23 November 2016, 18:24:45 UTC
8d5f157 Denis Yuen 23 November 2016, 18:22:48 UTC Iterate versions for staging testing 23 November 2016, 18:22:48 UTC
6aa181f Andrew Duncan 21 November 2016, 20:14:53 UTC Feature/multiple test json (#500) This updates the test json support so that it supports multiple test jsons per entry version. 21 November 2016, 20:14:53 UTC
f29a604 Andrew Duncan 18 November 2016, 16:49:10 UTC Feature/wdl file prov for dirs (#499) This fixes WDL file prov during launch so that it does not fail if an input file is a directory. Instead it just creates an associated directory in the directory where we put cromwell input (cromwell-input/hash/). When copying files/dirs to the cromwell-input dir, we will also maintain the directory structure, as before we just put all of the input files into the same directory. 18 November 2016, 16:49:10 UTC
b757279 Denis Yuen 18 November 2016, 15:47:52 UTC Feature/directory fix (#497) * Add fix for local directories as input and output (Ignore them for the purposes of file provisioning) * Update cwlavro to properly generate stubs for directories * Add tests for directory conversion and run 18 November 2016, 15:47:52 UTC
c93d19f Andrew Duncan 18 November 2016, 15:16:35 UTC Feature/verify for entry versions (#496) Alters verification so that it is based on a version and not an entry overall. 18 November 2016, 15:16:35 UTC
2567ff2 Denis Yuen 16 November 2016, 20:11:14 UTC Remove superfluous nested seqware workflow 17 November 2016, 17:20:33 UTC
1ff8691 Denis Yuen 16 November 2016, 19:42:04 UTC Add an option to convert to yaml 17 November 2016, 17:20:33 UTC
26f4bf9 Denis Yuen 16 November 2016, 18:32:54 UTC Attempt to suppress un-necessary builds (#491) * Suppress un-necessary build coverage 16 November 2016, 18:32:54 UTC
981d88b Denis Yuen 15 November 2016, 19:43:45 UTC Do a proper cleanup 15 November 2016, 21:54:22 UTC
07fcfb9 Denis Yuen 15 November 2016, 19:11:11 UTC Add check for cwltool and schema-salad dependencies #487 15 November 2016, 21:54:22 UTC
41116f0 Denis Yuen 14 November 2016, 20:31:43 UTC Hack around JAVA_HOME broken on Travis 15 November 2016, 21:54:22 UTC
5ba0556 Denis Yuen 14 November 2016, 20:05:25 UTC Follow-up on #479, next step verified versions! 15 November 2016, 21:54:22 UTC
bc6c646 Denis Yuen 14 November 2016, 19:42:53 UTC Update for #477 15 November 2016, 21:54:22 UTC
4c64bd8 Denis Yuen 14 November 2016, 17:12:35 UTC Handle format and default flags while updating cwltool 15 November 2016, 21:54:22 UTC
5453093 Andrew Duncan 10 November 2016, 18:36:49 UTC Feature/verified entries (#479) This adds support for admins to be able to verify entries. 10 November 2016, 18:36:49 UTC
443180a Denis Yuen 08 November 2016, 16:39:11 UTC Merge branch 'master' into develop 08 November 2016, 16:39:11 UTC
3398616 Denis Yuen 04 November 2016, 16:37:26 UTC Feature/attempt wdl4s update (#465) * update wdl4s to 0.6 * Issue with broken HEAD requests https://issues.apache.org/jira/browse/VFS-560 Affects getting files from current ICGC-portal * Update bridge code to match existing integration tests 04 November 2016, 16:37:26 UTC
2020fc1 Andrew Duncan 04 November 2016, 14:31:31 UTC wdl file provisioning only generates one hash for new file dir, also names files the same as in the original json (#464) 04 November 2016, 14:31:31 UTC
985c90e Andrew Duncan 03 November 2016, 20:51:16 UTC Feature/travis env testing (#466) * split up coverage build from regular build 03 November 2016, 20:51:16 UTC
2f03b6f Andrew Duncan 03 November 2016, 14:59:12 UTC Feature/test json support (#458) * support for test json/yml files for a tool/workflow * only one test json per descriptor type per version, in the future will support multiple test json per descriptor type per version 03 November 2016, 14:59:12 UTC
5846cf1 Denis Yuen 02 November 2016, 18:18:02 UTC Feature/wdl refactor update (#462) * Refactor to use external cromwell and update to 0.21 * Add to tests and unwrap exit code 02 November 2016, 18:18:02 UTC
c739468 Denis Yuen 01 November 2016, 20:46:13 UTC No longer needed (#459) 01 November 2016, 20:46:13 UTC
4f50d6c Denis Yuen 28 October 2016, 17:17:18 UTC Update README.md 28 October 2016, 17:17:18 UTC
c654cfb Andrew Duncan 24 October 2016, 21:02:05 UTC Feature/wdl dag improvements (#451) * Upgrading DAG for WDL to match functionality of CWL DAGs * WDL parser now resolves imports that are HTTP/HTTPS or local files (note that Cromwell does not currently support HTTP/HTTPS imports) 24 October 2016, 21:02:05 UTC
1b12b95 Andrew Duncan 14 October 2016, 21:40:27 UTC Feature/dag refactor (#441) * More information passed in DAG json * Moved DAG code to its own class 14 October 2016, 21:40:27 UTC
bf9f6e8 Andrew Duncan 12 October 2016, 20:02:00 UTC Feature/gitlab sourcecoderepo support (#440) * Added support for GitLab as a source code repo * Added tests for GitLab 12 October 2016, 20:02:00 UTC
471dced Denis Yuen 07 October 2016, 19:35:06 UTC [maven-release-plugin] prepare for next development iteration 07 October 2016, 19:35:06 UTC
6d4405a Denis Yuen 07 October 2016, 19:34:17 UTC [maven-release-plugin] prepare release 1.1-alpha.0 07 October 2016, 19:34:17 UTC
b08d421 Denis Yuen 07 October 2016, 19:28:27 UTC Feature/consonance compat (#438) * Allow dockstore tool/workflow launch to stream output * Clean up optional and allow stream passthrough * Re-organize client to hook up Consonance 07 October 2016, 19:28:27 UTC
d07a56c Andrew Duncan 07 October 2016, 17:19:15 UTC Feature/dag improvements (#436) * Creates DAG using CWL Avro instead of YAML parser * DAG order for CWL is now based off of order of execution * Tests updated/added 07 October 2016, 17:19:15 UTC
6475cc4 Denis Yuen 03 October 2016, 20:16:35 UTC Hotfix/ga4gh validation (#432) * Iterate projection version * Deal with validation error for GA4GH Use 0 time to deal with unknown times * Also ensure that tool meta-version is non-null 03 October 2016, 20:16:35 UTC
fc75f4d Andrew Duncan 29 September 2016, 15:55:25 UTC Feature/blank descriptor (#425) * Can no longer manually publish or update a tool on the command line without at least one descriptor path set * Added support for dirty bit for versions * Updated migrations to add dirtybit column 29 September 2016, 15:55:25 UTC
730edc3 Andrew Duncan 26 September 2016, 15:02:03 UTC Feature/refresh tool refactoring (#422) Refactored tool refresh so that it is easier to update/understand. 26 September 2016, 15:02:03 UTC
c829c34 Denis Yuen 23 September 2016, 15:19:49 UTC Update to CWL 1.0 (#424) 23 September 2016, 15:19:49 UTC
65f701a Andrew Duncan 20 September 2016, 19:17:03 UTC Feature/refresh refactor (#400) Restructures how workflows are refreshed to make the code cleaner and easier to extend functionality and add new git hosts. 20 September 2016, 19:17:03 UTC
de69f56 Andrew Duncan 20 September 2016, 18:08:38 UTC Restubbing a workflow now sets the labels (#421) Labels will persist after restubbing a workflow. 20 September 2016, 18:08:38 UTC
be658f1 Denis Yuen 19 September 2016, 14:22:11 UTC Update README.md 19 September 2016, 14:22:11 UTC
70c1eed Denis Yuen 16 September 2016, 17:30:32 UTC Merge tag '1.0' [maven-release-plugin] copy for tag 1.0 16 September 2016, 17:30:32 UTC
8939f29 Denis Yuen 16 September 2016, 17:30:04 UTC Merge branch 'release/1.0' into develop 16 September 2016, 17:30:04 UTC
4e88e37 Denis Yuen 16 September 2016, 17:23:16 UTC [maven-release-plugin] prepare for next development iteration 16 September 2016, 17:23:16 UTC
a2257b3 Denis Yuen 16 September 2016, 17:23:13 UTC [maven-release-plugin] prepare release 1.0 16 September 2016, 17:23:13 UTC
42bffb2 Denis Yuen 14 September 2016, 14:39:44 UTC [maven-release-plugin] prepare for next development iteration 14 September 2016, 14:39:44 UTC
1b784ff Denis Yuen 14 September 2016, 14:39:41 UTC [maven-release-plugin] prepare release 1.0-rc.2 14 September 2016, 14:39:41 UTC
34c2629 Denis Yuen 13 September 2016, 21:14:23 UTC Merge branch 'release/1.0' of github.com:ga4gh/dockstore into release/1.0 13 September 2016, 21:14:23 UTC
1fa72b0 Denis Yuen 13 September 2016, 21:13:57 UTC Search for and allow doc to override description 13 September 2016, 21:13:57 UTC
d2cea93 Denis Yuen 13 September 2016, 21:13:42 UTC Typo 13 September 2016, 21:13:42 UTC
00becd0 Denis Yuen 13 September 2016, 19:56:05 UTC Correct migrations.xml 13 September 2016, 19:56:05 UTC
06511f2 Denis Yuen 13 September 2016, 19:31:43 UTC [maven-release-plugin] prepare for next development iteration 13 September 2016, 19:31:43 UTC
1932203 Denis Yuen 13 September 2016, 19:31:40 UTC [maven-release-plugin] prepare release 1.0-rc.1 13 September 2016, 19:31:40 UTC
a986da6 Denis Yuen 13 September 2016, 19:26:44 UTC Feature/late breaking ga4gh tool registry changes (#401) * Update generated files * Superficial implementation * Fix up odd case-changes to GA4GH classes * Clarify readme * update secret archive * Update encrypted archive with new token * Add migration.xml for default branch for testing 13 September 2016, 19:26:44 UTC
dc3e0df Denis Yuen 12 September 2016, 21:09:17 UTC [maven-release-plugin] prepare for next development iteration 12 September 2016, 21:09:17 UTC
269c1ee Denis Yuen 12 September 2016, 21:09:14 UTC [maven-release-plugin] prepare release 1.0-rc.0 12 September 2016, 21:09:14 UTC
65724fe Denis Yuen 12 September 2016, 21:00:00 UTC Iterate version number 12 September 2016, 21:00:00 UTC
85c45ab Denis Yuen 12 September 2016, 20:57:46 UTC Iterate versions 12 September 2016, 20:57:46 UTC
9253e28 Denis Yuen 12 September 2016, 19:00:41 UTC Iterate version numbers 12 September 2016, 19:00:41 UTC
4914369 Denis Yuen 12 September 2016, 18:28:49 UTC Iterate version number for release 12 September 2016, 18:28:49 UTC
3ae4322 Andrew Duncan 12 September 2016, 18:26:50 UTC Added support for extra CWLtool flags from the config file (#397) * Added support for extra CWLtool flags from the config file * Removed redundant function passing * Cleaner approach to adding extra cwltool flags 12 September 2016, 18:26:50 UTC
dc377f8 Andrew Duncan 07 September 2016, 14:07:05 UTC Feature/default branch support (#395) -added support for a default branch (github/bitbucket) -removed valid trigger from code (seems to have little value, also doesn't do what we want) -other small bugfixes 07 September 2016, 14:07:05 UTC
30cea93 Denis Yuen 02 September 2016, 14:36:08 UTC Allow use of yaml parameter files (#393) 02 September 2016, 14:36:08 UTC
4d052dd Denis Yuen 30 August 2016, 15:14:34 UTC Disable client for oddly formatted resource until swagger-codegen update (#387) 30 August 2016, 15:14:34 UTC
6eedf63 Denis Yuen 23 August 2016, 21:03:01 UTC Document bitbucket 23 August 2016, 21:03:01 UTC
e9a5910 Denis Yuen 18 August 2016, 14:32:21 UTC [maven-release-plugin] prepare for next development iteration 18 August 2016, 14:32:21 UTC
dc17238 Denis Yuen 18 August 2016, 14:32:17 UTC [maven-release-plugin] prepare release 0.4-beta.7 18 August 2016, 14:32:17 UTC
f92cb1c Denis Yuen 18 August 2016, 14:24:10 UTC Forgot to override response (#381) 18 August 2016, 14:24:10 UTC
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