Cromwell 83 #22
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Cromwell 83 #22
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This reverts commit 5c98d38.
* wip * wip * wip * wip * checkpoint * wip * wip * wip * wip * wip * compiles??? * cleanup * grrr * fix test * fix test * fix bug in choosing default language factory * fix tests * sheesh * oops * some test fixes, some commenting out * fix ordering * forcing with some [force ci] * temporarily comment out more problematic varargs stuff * fix test * why do I have to do [force ci] to get most sub-builds to run? * wip, varargs broken * yaass * checkpoint * checkpoint [force ci] * more [force ci] * restore comment * grrr * grrr [force ci] * cleanup * debug attempt * force debug * grrr * restructure * fixy fix? * cleanup * oops * Revert "debug attempt" This reverts commit 59b4e01. * Revert "force debug" This reverts commit 6b1fba2. * sweepy sweep * try * more * wip * docs * Scala 2.13 codegen fixes * oops * PR feedback * PR feedback * PR feedback * CI bump * Poke CI * Unpoke CI Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
…3] (broadinstitute#6725) * Fix call cache checks in case of cache invalidation [CROM-6603] * Add tests for call caching skipping good hits * Update changelog Co-authored-by: Nikita Myazin <myazin.n@list.ru> Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
* bad stdout location tests * just a draft * checkStdout helper function * Adding stderr wdl and test files, refactoring functions and adding functions to handle stderr * Fixing error messages * bad stdout location tests * just a draft * checkStdout helper function * Adding stderr wdl and test files, refactoring functions and adding functions to handle stderr * Fixing error messages * Rebasing * Rebasing * Omitting the metadata section for Travis builds to pass * Bw 1126 workflow level stdout / stderr expressions fail, hang execution forever (broadinstitute#6745) * Combining similar-use functions * All tests created * Saving changes * Adding unit tests * Update wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> * Update wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> * Update wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> * Update wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> * Changing to more general function naming * Return type change for functions * Reverting Saloni newline addition * Reverting Saloni newline addition and fixing return type * bad stdout location tests * just a draft * checkStdout helper function * Adding stderr wdl and test files, refactoring functions and adding functions to handle stderr * Fixing error messages * Rebasing * Omitting the metadata section for Travis builds to pass * Bw 1126 workflow level stdout / stderr expressions fail, hang execution forever (broadinstitute#6745) * Combining similar-use functions * All tests created * Saving changes * Adding unit tests * Update wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> * Update wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> * Update wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> * Update wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> * Changing to more general function naming * Return type change for functions * Reverting Saloni newline addition * Reverting Saloni newline addition and fixing return type * Revert "Reverting Saloni newline addition and fixing return type" This reverts commit 858214d. Reverting for Travis CI tests * Reverting Saloni newline addition and fixing return type * remove_tests * remove_corresponding_wdl_files * Updating some unit tests with more correct functionality * Fixing missed input for Invalid function * triggering build Co-authored-by: Chris Llanwarne <cjllanwarne@gmail.com> Co-authored-by: Saloni Shah <salonipshah11@gmail.com> Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
…Swagger (broadinstitute#6749) * Saving changes * Saving changes * Adding and deleting endpoints * Saving changes * Service-info, cancel, and status endpoints added. * WES enpoints have api prefix * Update yaml file and apidocs * Directed response for new endpoints to existing response options; omitted lines that caused the associated spec file to fail in one of its tests * Adding newline in .yaml and adding the RESTAPI.md file to gitattributes. * Adding newline in .yaml and adding the RESTAPI.md file to gitattributes. * Updating CHANGELOG.md * Update CHANGELOG.md Co-authored-by: Adam Nichols <anichols@broadinstitute.org> Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
* Removed Wes2Cromwell project, added 'runs' endpoint a necessary functions. * saving... * saving... * saving... * saving... * Fix missing JSON implicits * Added endpoint to cromwell.yaml and added api prefix * Getting rid of unnecessary implicits * Fixing and changing function name * Updated RESTAPI.md, cromwell.yaml, and RunListResponse.scala * Getting rid of comments * Omitting unexpected arguments * Removing headers, adding further details in cromwell.yaml * Updating description and RESTAPI.md * saving... * saving... * saving... * saving... * saving... * Moving functions to consolidate, updating CHANGELOG.md, deleting Wes2CromwellInterface.scala file * Updated CHANGELOG.md, passed error message to API * saving... * Update CHANGELOG.md Co-authored-by: Adam Nichols <anichols@broadinstitute.org> * Update engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala Co-authored-by: Adam Nichols <anichols@broadinstitute.org> * Update engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala Co-authored-by: Adam Nichols <anichols@broadinstitute.org> * Changes to CHANGELOG.md, updating routes * Unused imports * Cleanup * Cleanup * codecov * . * . Co-authored-by: Adam Nichols <aednichols@gmail.com> Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
* implement reversed ordering for start and end keys * add unit test for new timestamp ordering * more coverage in unit test
This reverts commit d0a18a5.
This reverts commit d424c3c.
This reverts commit 13eecc9.
This reverts commit 9c1f2f0.
* Add TES tags to release notes * Poke CI * Debug logging for build * Fix release version * Remove incorrect release log entry * Back out debug changes * poke ci * poke ci
* BT-614 Remove Alibaba/Aliyun backend * BT-614 Correct dependancies for docker hashing * BT-614 Remove OSS from ServiceInfoSpec * BT-614 Remove OSS references in a few last files * BT-614 removing some dangling references to BCS and correcting change log * BT-614 Updated changelog for clarity
Updated GoogleCloudStorage to 2.9.2
* Add release notes for Cromwell 82 * Specify upgrade version * Fix library name Co-authored-by: Adam Nichols <anichols@broadinstitute.org> Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
BT-684 Initial Blob Storage Implementation Merge the initial PathBuilder and PathBuilderFactory for accessing blob storage
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