https://github.com/ga4gh/dockstore

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Revision Author Date Message Commit Date
000ed1c [maven-release-plugin] prepare release 1.6.0-rc.3 02 April 2019, 14:44:09 UTC
eb8de1d Merge branch 'release/1.6.0' into absolute_path_better_guess 02 April 2019, 14:40:59 UTC
b3b1a71 WES CLI improvements (#2315) * fix WDL WES launch * add local entry flag * remove print stacktrace * add comments on WDL version Github issue #2315 01 April 2019, 23:25:31 UTC
215494b Looks like some code depends on this 01 April 2019, 21:11:00 UTC
ae0ff58 update entry publish --help on CLI (#2310) #1216 * update help message for entry publish * for workflow client removed --entryname parameter and cleaned up handlePublishUnpublish() * abstracted publishHelp(), overridden in workflow and tool clients 01 April 2019, 20:31:31 UTC
64283df Actually run the tests? 01 April 2019, 19:42:19 UTC
882f074 Better migration guess for absolute paths 01 April 2019, 19:24:03 UTC
554a3d3 [maven-release-plugin] prepare for next development iteration 29 March 2019, 18:50:14 UTC
2ca6d00 [maven-release-plugin] prepare release 1.6.0-rc.1 29 March 2019, 18:50:03 UTC
f123587 Feature/2303/refresh fix (#2319) * Grab all repos, but use full name and not name 29 March 2019, 17:27:32 UTC
2f0d46e Merge branch 'develop' into release/1.6.0 29 March 2019, 15:13:45 UTC
be1f537 Merge tag '1.5.5' into develop 1.5.5 29 March 2019, 15:07:42 UTC
b9ff3d6 Merge branch 'hotfix/1.5.5' 29 March 2019, 15:03:28 UTC
065bf4f Change error message (#2298) 27 March 2019, 13:05:18 UTC
abceab0 only return published entries for a collection (#2289) 26 March 2019, 18:57:47 UTC
f8fe596 CVE update (#2276) * not particularly critical until we use RDS 26 March 2019, 16:57:04 UTC
e7dad6e [maven-release-plugin] prepare for next development iteration 26 March 2019, 14:48:24 UTC
10b4f31 [maven-release-plugin] prepare release 1.6.0-rc.0 26 March 2019, 14:48:18 UTC
70842ba Change default server url (#2277) 26 March 2019, 14:43:30 UTC
1ad1113 Fix this self-link (#2278) 26 March 2019, 14:19:15 UTC
2249452 Feature/2118/checker workflow indexing (#2234) * Feature/1973/remove checker workflows in search (#2006) * Quick fix to remove checker workflows * Fix + small test * More consistent * Simplification * Test enhancement * Remove ga4ghValidateTest and sleeps to Search test * Add a sleep function to avoid repetition * Feature/updated tokens (#2169) * update secret archive * New folder name Note: this was an update for the GitHub tokens only. 25 March 2019, 20:55:07 UTC
4617f62 switch keywords in WES help (#2275) 25 March 2019, 20:45:05 UTC
d7c78f1 provisioning input to handle paths with spaces (#2262) #1663 * provision inputfile to handle paths with spaces * update method names, add integration test * switch to escaper, add runClientCommandConfig() to run tests with specified config file 25 March 2019, 19:39:46 UTC
eb65854 Reject some alias prefixes (#2273) * we probably want to keep these ones for future use 25 March 2019, 18:33:17 UTC
d3bf79f Feature/2085/absolute path check (#2239) * Add constraint * Make new sourcefile add a '/' * Allow empty absolutepath * Hacky workaround * Fix 25 March 2019, 18:17:15 UTC
395eb91 Add sleeps to ES tests to wait for reindex (#2271) 25 March 2019, 17:49:52 UTC
4da6843 Remove explicit port (#2266) * Remove explicit port #1594 The final vestige! 22 March 2019, 16:24:31 UTC
501d499 Update checkstyle due to warning (#2263) 21 March 2019, 17:04:02 UTC
11aa00f Honor version limit when posting zip (#2256) #2092 Found when verifying #2092. 20 March 2019, 22:21:15 UTC
09803ef Release/1.6.0 beta.4 (#2253) * [maven-release-plugin] prepare release 1.6.0-beta.4 * [maven-release-plugin] prepare for next development iteration 20 March 2019, 18:49:57 UTC
5052cd1 Hookup codacy based on (#2250) * Hookup codacy based on https://github.com/codacy/codacy-coverage-reporter#setup * Hardcode, looks like this rate limits https://github.com/codacy/codacy-coverage-reporter/issues/75 20 March 2019, 15:44:18 UTC
e55a604 Add display names to object (#2246) * Add display names to object * Add assertions 20 March 2019, 12:31:17 UTC
e24f884 Handle null case properly for nextflow descriptions (#2248) 20 March 2019, 02:30:30 UTC
ddc2a1e Feature/request re review (#2245) * can request organization re-review on rejected organizations 19 March 2019, 23:08:37 UTC
c849421 [skip travis] (#2238) 19 March 2019, 14:40:59 UTC
fc83586 coverage only experiment (#2237) * experiment * regression-integration-tests need java 8 19 March 2019, 14:40:47 UTC
eb04213 do not include version in rss (#2229) 15 March 2019, 19:14:58 UTC
3d3ed0e Don't save token from authorization header (#2228) When Dockstore API is invoked with a Google token, we look up the user based on the email associated with that token. If we don't find a user, we create one. Then we would save the token along with the user; this was done to use that token to authenticate subsequent API calls to SAM. Instead, don't persist the token to the database. Added a transient field to User to hold the token and when calls are made to SAM, check that field first. Not wild about changing the User class to not directly map to the database -- we don't use @Transient anywhere else. But this seems to be the lowest impact way of implementing this. 15 March 2019, 16:12:39 UTC
40ee223 swap put and post for collection resource (#2226) 15 March 2019, 15:31:29 UTC
74b69a9 Add help for WES commands and WES beta quality warning (#2224) Add help for Workflow Execution Service (WES) Dockstore CLI commands 14 March 2019, 19:38:28 UTC
6bd4b59 Release/1.6.0 beta.3 (#2222) * [maven-release-plugin] prepare release 1.6.0-beta.3 * [maven-release-plugin] prepare for next development iteration * new release 13 March 2019, 19:31:47 UTC
8eea323 Bump vfs2 past CVE issue with httpclient 3 (#2213) * Bump vfs2 past CVE issue with httpclient 3 * now banned, use httpclient 4 * Fix test 13 March 2019, 16:58:12 UTC
3472be3 Rename swagger to openapi (#2217) Rename swagger to openapi DOCK-574 13 March 2019, 15:33:15 UTC
bbc0cb6 ensure all absolute paths start with / (#2212) 13 March 2019, 12:39:49 UTC
213e3e3 Add documentation on converting from WES 1.0 swagger 2.0 to OpenAPI 3.0 (#2211) Add documentation on converting from Swagger 2.0 to OpenAPI 3.0 12 March 2019, 17:29:47 UTC
f8c5721 Feature/ignore unknown wdl methods (#2201) * Ignore unknown methods till a better WDL update * More ignore * PR feedback * Add warning message 12 March 2019, 16:03:40 UTC
ffbd89e Less misleading error message (#2210) 12 March 2019, 14:59:50 UTC
695badf Feature/small issues (#2208) * Rename org_aliases #2200 * Small fix for https://github.com/ga4gh/dockstore/issues/2164 * satisfy codacy with a net positive change 12 March 2019, 14:27:25 UTC
89923b4 Release/1.6.0 beta.2 (#2209) * [maven-release-plugin] prepare release 1.6.0-beta.2 * [maven-release-plugin] prepare for next development iteration * update openapi and swagger 11 March 2019, 17:19:22 UTC
11e785a [WIP] support for WES in the CLI (#2156) WES client implementation in Dockstore CLI 08 March 2019, 23:01:55 UTC
d5b0372 Feature/get collection by name (#2199) * collection json now included organizationName * added get collection by name * added tests for get collection by name 08 March 2019, 17:58:10 UTC
b015054 Feature/minor speed build (#2197) * move out build steps [skip travis] * don't use confidential config for propose_migration.sh * Don't duplicate UI tutorial 08 March 2019, 17:20:49 UTC
f30311f Change error message to be more helpful (#2198) 08 March 2019, 17:10:59 UTC
89267fc Feature/1915/update cwl tool version (#2146) * Update version handler * Add the updated requirements files * Test with new cwltool version * Update python3 deps (optional) * Update python2 deps (optional) * Fix for metadataApi using the wrong basepath 08 March 2019, 15:26:06 UTC
dd5fbd8 Feature/delete yourself (#2195) * validate email and link for orgs * cannot delete yourself if you are in an org 07 March 2019, 20:42:18 UTC
013ef1d Remove maven release steps from README (#2193) Doing a maven release is described in two places, here, and in internal documentation. Instead of maintaining the same info in two places and there being confusion as to which one to follow, I propose we just maintain the internal doc up to date and remove this info from the README. We can do it the other way around, if preferred. Please reject the associated PR if so. 07 March 2019, 18:21:05 UTC
0a4e625 Release/1.6.0 beta.1 (#2191) * [maven-release-plugin] prepare release 1.6.0-beta.1 * [maven-release-plugin] prepare for next development iteration * 1.6.0-beta.1 release 07 March 2019, 17:04:53 UTC
d244b02 Working on path creation issue (#2189) * Working on path creation issue * simplify with code from zip export * Add test based on original report * migration results in some odd absolute paths 07 March 2019, 16:27:38 UTC
c062e11 Feature/more org insensitivity (#2186) * fix migration * Extend to collections * allow collection names to be unique per org (but not display names) 06 March 2019, 17:57:41 UTC
e7ef1c7 Fix header links for #2153 (#2182) 05 March 2019, 20:52:07 UTC
3787984 Change OrgResource HTTP annotation and regenerate swagger (#2176) Changes PUT to POST for create and POST to PUT for update Issue #2176 05 March 2019, 19:41:37 UTC
045adcf Fix organization case switching renames (#2172) 05 March 2019, 15:30:48 UTC
d6a2038 Feature/2052/organization logo (#2144) Added avatarUrl column to organization table. Must end in .jpeg, .jpg, .png, or .gif. ga4gh/dockstore#2052 05 March 2019, 04:41:41 UTC
cf185bb Add per-user limits for hosted entries (#2159) #2092 04 March 2019, 20:45:25 UTC
70f33df Feature/updated tokens (#2169) * update secret archive * New folder name Note: this was an update for the GitHub tokens only. 04 March 2019, 17:02:14 UTC
c1a8d7c [maven-release-plugin] prepare for next development iteration 28 February 2019, 22:40:37 UTC
3cd46a0 [maven-release-plugin] prepare release 1.6.0-beta.0 28 February 2019, 22:40:31 UTC
026e83f Feature/more alias (#2152) * Cleanup (there's a lot of duplicate/copy-paste code in here) * Transient parent reference in organizations 28 February 2019, 22:20:34 UTC
137f86c Create a new version of a hosted workflow with Zip (#2148) #1768 Allows a user to submit a zip file to add a new version to a hosted workflow. The zip file needs to contain a .dockstore.yml in its root directory that describes the contents of the zip. See the DockstoreYaml.java class for expected fields. I was initially going to do by submitting an application/octet-stream, but Swagger 2 codegen does not generate correct code for client libraries. See https://swagger.io/docs/specification/2-0/file-upload/. Making it a multipart/form-data allows users to hit the UI from the Swagger UI. The code ZipSourceFileHelper.java guards against "zip bomb" attacks. Unfortunately we can only see the size of the uncompressed entries in a zip by writing to a file -- reading from the payload directly in memory doesn't reliably give the sizes. Todos Should support a workflowVersion value in .dockstoreYaml, which will tag the revision accordingly. The code currently makes assumptions about the name field always being a number. See AbstractHostedEntryResourceName.calculateNextVersionName. UI does not show .dockstore.yml. DockstoreYaml.java is just a beginning and not really generic enough yet. 28 February 2019, 21:43:30 UTC
9ceb049 Release/1.6.0 alpha.7 (#2151) * [maven-release-plugin] prepare release 1.6.0-alpha.7 * [maven-release-plugin] prepare for next development iteration * udpate version 28 February 2019, 17:39:13 UTC
9c9a05d Add pagination to events API (#2150) * Add pagination to events API #2122 28 February 2019, 01:58:16 UTC
a522bc2 added topic to collection, also some collection description endpoints (#2149) * added topic to collection, also some collection description endpoints 27 February 2019, 15:43:17 UTC
fffa520 added org and collection display name and migrations (#2143) * added organisation and collection display name and migrations 26 February 2019, 18:18:48 UTC
db7890a Feature/force db consistency (#2131) * Enforce database consistency * Hook up new stage 25 February 2019, 20:12:26 UTC
d54cbb7 Feature/1891/cromwell for cwl (#2126) * Reorganisation of clients and launchers * Can run CWL tools/workflows with Cromwell 25 February 2019, 19:34:36 UTC
0ff6f0f Feature/circle ci (#2136) * Try this cache setup * Need different Docker image https://stackoverflow.com/questions/53010200/maven-surefire-could-not-find-forkedbooter-class/53085816#53085816 * another attempt to collect surefire results * Restore cache properly 22 February 2019, 23:08:24 UTC
186af38 Feature/circle ci (#2136) * Try this cache setup * Need different Docker image https://stackoverflow.com/questions/53010200/maven-surefire-could-not-find-forkedbooter-class/53085816#53085816 * another attempt to collect surefire results * Restore cache properly 22 February 2019, 21:55:26 UTC
0e9b4e1 Feature/get entry collection organization (#2096) * Get collections for entries * Add assertions * Merge fixes * Re-adding the yamls * Fix? * Change object properties 19 February 2019, 16:56:09 UTC
bc44978 change TRS v1 response objects to correctly reflect v1 in url. Added unit tests. (#2101) #1849 When given a GA4GHV1 api request, the tool would first create a v2 objects then would convert to V1 objects. In this process the url wasn't handled to reflect v1 in the response, but otherwise the code worked. This fix includes adding a change in the conversion to correctly reflect v1 in urls of a ga4gh/v1 request. Also added unit tests. A v1 api request now correctly returns a v1 url response. A v2 api request still correctly returns a v2 url response. 13 February 2019, 17:51:21 UTC
d4e776f Feature/stabilize openapi (#2100) * Try to stabilize openapi generation * While at it, stop import order from changing 12 February 2019, 18:44:21 UTC
9e43a8a Generate a non-null version for test clients (#2097) * Generate a non-null version for test clients * helps distinguish our CI builds too 11 February 2019, 21:15:03 UTC
2bd1ade provide error messages concerning workflow version (#2086) provide error messages concerning workflow version resolves #1813 11 February 2019, 16:46:44 UTC
6253be6 Release/1.6.0 alpha.6 (#2099) * [maven-release-plugin] prepare release 1.6.0-alpha.6 * [maven-release-plugin] prepare for next development iteration * bump version 09 February 2019, 23:08:24 UTC
9dfe42e Migration was not removing null values (#2094) #2093 Running migrations was not removing null value from absolutepath row, and the addNotNullConstraint would then fail. Changed to use the `<update>` element. 08 February 2019, 19:41:17 UTC
61512ef Working on imports defined in config files (#2071) 08 February 2019, 18:20:28 UTC
41e744d Rename organization (#2090) * Had to be done 08 February 2019, 17:20:51 UTC
2b1de27 Constrain unique organization names (#2091) * make get case insensitive 07 February 2019, 16:58:51 UTC
e974543 Feature/add user to org by username error (#2087) * check that user exists before adding to org * test that you cannot add a user to org by username when username does not exist 06 February 2019, 20:46:57 UTC
50f2c77 Provide Cromwell stdout and stderr to console (#2083) 06 February 2019, 18:41:13 UTC
799a0e5 Release/1.6.0 alpha.5 (#2076) * fix snapshot versions * [maven-release-plugin] prepare release 1.6.0-alpha.5 * [maven-release-plugin] prepare for next development iteration 02 February 2019, 22:33:10 UTC
4476609 Feature/more organisation endpoint fixes (#2075) * fix collection and org endpoint * update tests with new fixes 01 February 2019, 16:25:58 UTC
7727ba6 Release/1.6.0 alpha.4 (#2054) * [maven-release-plugin] prepare release 1.6.0-alpha.4 * [maven-release-plugin] prepare for next development iteration * updated swagger 01 February 2019, 16:03:44 UTC
aacc1b4 Feature/nextflow config update (#2053) * Use Nextflow to parse config files * possible improvements to performance in comments * added nfl core tests * updated groovy to match nextflow dependency 31 January 2019, 18:47:16 UTC
7765adf Feature/bounded swagger upgrade (#2045) * Update swagger-ui * includes many OpenAPI 3.0 fixes, probably useful * Minimum config to serve up swagger 2.0 + openapi 3.0 * Generate openapi.json at build time works! * Demo adding OpenAPI3 annotations 31 January 2019, 15:17:25 UTC
d82c3b9 Add user to organization (#2051) 29 January 2019, 20:44:57 UTC
aad44ed Organisation state change from boolean to an enum, plus small changes for requests (#2044) * organizations can now be approved, pending or rejected * tests for new states * added an endpoint for retrieving all orgs a that a user belongs to * some org api changes from the requests page * tests for new endpoint * cannot reject an approved organization 29 January 2019, 18:46:38 UTC
c7ae19b Ensure absolute path always set for hosted workflows (#2049) #2040 Issue is written up as a problem with downloading zips; this is because it's a fallout of the absolute path not being set. 28 January 2019, 21:19:46 UTC
94890a5 Feature/put markdown (#2042) * Add get and put endpoint for description 25 January 2019, 21:11:48 UTC
e61c0c0 sort events in descending order (#2047) 25 January 2019, 19:59:42 UTC
227fedd Don't log error when saving a non-published workflow (#2039) #2034 Saving a new hosted workflow version calls `ElasticManager.handleIndexUpdate`, which would cause an error to be logged if the the workflow is not published. Log it at info level instead, since it's not an error condition. The other option is to not call the method at all if the workflow is not published, but the method is called from several places, and that seemed slightly riskier. Also noticed that if there is an error in the response from the ElasticManager, that wasn't being logged at the error level. 23 January 2019, 19:19:42 UTC
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