dockstore/dockstore: 1.13.0

Highlighted new features performance improvements for GA4GH TRS and for UI display for workflows with many versions cwltool and cromwell support update improved display of github app logs before first successful registration to aid debugging improved validation and debugging display for workflows with a partially correct .dockstore.yml bugfixes for searching full-text, workflows without authors, search display for starred workflows deployment improvements behind-the-scenes to allow for drift detection, between release deployment of supporting infrastructure # Breaking changes none intended Full Changelog changes to support Snakemake by @wshands in https://github.com/dockstore/dockstore/pull/4686 Update README.md by @denis-yuen in https://github.com/dockstore/dockstore/pull/4708 Disable this test till we get TRS working with both paging and apptools by @denis-yuen in https://github.com/dockstore/dockstore/pull/4726 Add LGTM suppression comment for false positive by @david4096 in https://github.com/dockstore/dockstore/pull/4725 Bump postgresql from 42.2.25 to 42.3.3 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/4733 bump cromwell artifacts versions and dependencies by @wshands in https://github.com/dockstore/dockstore/pull/4759 Remove language specific code to simplify adding a new language by @wshands in https://github.com/dockstore/dockstore/pull/4757 don't ignore get over 500 tags test by @wshands in https://github.com/dockstore/dockstore/pull/4780 Feature/java 17 finally by @denis-yuen in https://github.com/dockstore/dockstore/pull/4792 builds with CI friendly versions by @denis-yuen in https://github.com/dockstore/dockstore/pull/4789 switch to temurin image for Java 17 by @denis-yuen in https://github.com/dockstore/dockstore/pull/4806 Update swagger/openapi clients and plugins by @denis-yuen in https://github.com/dockstore/dockstore/pull/4799 Feature/checkstyle spotbugs update by @denis-yuen in https://github.com/dockstore/dockstore/pull/4807 dependabot.yml fine tune by @denis-yuen in https://github.com/dockstore/dockstore/pull/4809 Regression test with 1.10 by @coverbeck in https://github.com/dockstore/dockstore/pull/4824 typo by @denis-yuen in https://github.com/dockstore/dockstore/pull/4826 Bump char0n/swagger-editor-validate from 1.2.1 to 1.3.1 by @dependabot in https://github.com/dockstore/dockstore/pull/4828 Bump actions/checkout from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/4827 Bump actions/cache from 1 to 3.0.1 by @dependabot in https://github.com/dockstore/dockstore/pull/4829 Allow query parameter to load user profiles by @Richard-Hansen in https://github.com/dockstore/dockstore/pull/4837 aws encryption now with v2 support by @denis-yuen in https://github.com/dockstore/dockstore/pull/4841 Bump actions/setup-java from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/4846 Bump actions/cache from 3.0.1 to 3.0.2 by @dependabot in https://github.com/dockstore/dockstore/pull/4849 try out latest dropwizard patch by @denis-yuen in https://github.com/dockstore/dockstore/pull/4847 used descriptor and new galaxy default desc name by @wshands in https://github.com/dockstore/dockstore/pull/4825 bump cwltool version support by @wshands in https://github.com/dockstore/dockstore/pull/4848 move out to github actions by @denis-yuen in https://github.com/dockstore/dockstore/pull/4850 Feature/dock 2105/log negative validations in GitHub apps logs by @svonworl in https://github.com/dockstore/dockstore/pull/4844 Update deploy_snapshot.yml by @denis-yuen in https://github.com/dockstore/dockstore/pull/4864 Rename user_profile bio to link and sync GitHub bio by @kathy-t in https://github.com/dockstore/dockstore/pull/4865 optimize github apps log retrieval for common cases by @svonworl in https://github.com/dockstore/dockstore/pull/4861 improve performance of fetching descriptor file via trs by @svonworl in https://github.com/dockstore/dockstore/pull/4866 Convert empty string names and links in user profiles to null by @kathy-t in https://github.com/dockstore/dockstore/pull/4868 Add security policy markdown by @david4096 in https://github.com/dockstore/dockstore/pull/4869 fix circleci by @svonworl in https://github.com/dockstore/dockstore/pull/4891 DOCK-2105: change GitHub apps log separator to newlines by @svonworl in https://github.com/dockstore/dockstore/pull/4895 Bump docker/login-action from 1 to 2 by @dependabot in https://github.com/dockstore/dockstore/pull/4899 Bump docker/build-push-action from 2 to 3 by @dependabot in https://github.com/dockstore/dockstore/pull/4900 remove context from unit tests by @denis-yuen in https://github.com/dockstore/dockstore/pull/4903 Use integer offsets on /published endpoints (SEAB-3979) by @amarjandu in https://github.com/dockstore/dockstore/pull/4896 Update PULL_REQUEST_TEMPLATE.md by @denis-yuen in https://github.com/dockstore/dockstore/pull/4898 Query events by user id by @Richard-Hansen in https://github.com/dockstore/dockstore/pull/4901 Modified config.yml so that it sends coverage results for the unit test to codecov by @fhembroff in https://github.com/dockstore/dockstore/pull/4905 just reissue the tokens and see what happens by @denis-yuen in https://github.com/dockstore/dockstore/pull/4911 DOCK-2033: fix cwl hint precedence by @svonworl in https://github.com/dockstore/dockstore/pull/4912 Feature/flynn/4268/seperate bitbucket tests by @fhembroff in https://github.com/dockstore/dockstore/pull/4913 bring us into dropwizard 2.1 by @denis-yuen in https://github.com/dockstore/dockstore/pull/4919 Bump actions/cache from 3.0.2 to 3.0.3 by @dependabot in https://github.com/dockstore/dockstore/pull/4938 Add pattern validation for /metadata/runner_dependencies (#SEAB-3980) by @amarjandu in https://github.com/dockstore/dockstore/pull/4915 Feature/seab 4046/fix messagebodywriter exception by @svonworl in https://github.com/dockstore/dockstore/pull/4937 Updated the version numbers on several google clients by @fhembroff in https://github.com/dockstore/dockstore/pull/4942 Bump actions/cache from 3.0.3 to 3.0.4 by @dependabot in https://github.com/dockstore/dockstore/pull/4943 Standardize OpenAPI security field (#4671) by @amarjandu in https://github.com/dockstore/dockstore/pull/4944 Feature/seab 3896/remove trs caching code by @svonworl in https://github.com/dockstore/dockstore/pull/4949 Simplify language support by @wshands in https://github.com/dockstore/dockstore/pull/4940 re-create snyk suggestion by @denis-yuen in https://github.com/dockstore/dockstore/pull/4958 Add apple silicon setup to readme by @wshands in https://github.com/dockstore/dockstore/pull/4955 new api to get cli version by @wshands in https://github.com/dockstore/dockstore/pull/4948 fix api links by @denis-yuen in https://github.com/dockstore/dockstore/pull/4965 hook up initiator user to events endpoint and test by @denis-yuen in https://github.com/dockstore/dockstore/pull/4960 update to official maven wrapper by @denis-yuen in https://github.com/dockstore/dockstore/pull/4959 restrict to tags for now by @denis-yuen in https://github.com/dockstore/dockstore/pull/4966 Feature/dock 2110/continue processing dockstore yml after error by @svonworl in https://github.com/dockstore/dockstore/pull/4924 Feature/seab 4083/parrallel tests by @fhembroff in https://github.com/dockstore/dockstore/pull/4970 Merge to develop sanity check by @coverbeck in https://github.com/dockstore/dockstore/pull/4986 Remove unused constructors (SEAB-4055) by @amarjandu in https://github.com/dockstore/dockstore/pull/4952 Update SEM_VER_STRING to support prereleases (#4981) by @amarjandu in https://github.com/dockstore/dockstore/pull/4982 order events by date by @denis-yuen in https://github.com/dockstore/dockstore/pull/4991 batch process index index creation by @denis-yuen in https://github.com/dockstore/dockstore/pull/4973 dropwizard 2.1.1 by @denis-yuen in https://github.com/dockstore/dockstore/pull/4988 Add non-empty constraints to user_profile table (#4871) by @amarjandu in https://github.com/dockstore/dockstore/pull/4994 Changed version number of hibernate-validator by @fhembroff in https://github.com/dockstore/dockstore/pull/5004 syntax github workflow by @denis-yuen in https://github.com/dockstore/dockstore/pull/5011 Bump commons-configuration2 from 2.7 to 2.8.0 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/4997 Bump actions/cache from 3.0.4 to 3.0.5 by @dependabot in https://github.com/dockstore/dockstore/pull/5020 SEAB-4269: Configurable SourceFile path restriction by @svonworl in https://github.com/dockstore/dockstore/pull/5005 Tweak new Sourcefile path-related integration test by @svonworl in https://github.com/dockstore/dockstore/pull/5022 pom simplification for how liquibase-core is included by @denis-yuen in https://github.com/dockstore/dockstore/pull/5021 support grab-bag of updates by @denis-yuen in https://github.com/dockstore/dockstore/pull/5032 Check if user exists in user endpoints by @kathy-t in https://github.com/dockstore/dockstore/pull/5031 Removed Liquibase Changeset Message from Output in CircleCI by @fhembroff in https://github.com/dockstore/dockstore/pull/5033 Update PR template by @coverbeck in https://github.com/dockstore/dockstore/pull/5034 Feature/restub snapshot by @denis-yuen in https://github.com/dockstore/dockstore/pull/5035 Fix failed openapi validation by @kathy-t in https://github.com/dockstore/dockstore/pull/5036 Don't terminate indexing after an indexing failure by @coverbeck in https://github.com/dockstore/dockstore/pull/5024 Fix collectionsLength for starred organizations by @coverbeck in https://github.com/dockstore/dockstore/pull/5038 SEAB-4403: Refactor user-level permissions checks by @svonworl in https://github.com/dockstore/dockstore/pull/4989 add test and hook up verified to collection endpoint by @denis-yuen in https://github.com/dockstore/dockstore/pull/5037 ninjaed by @denis-yuen in https://github.com/dockstore/dockstore/pull/5048 index source files properly and test by @denis-yuen in https://github.com/dockstore/dockstore/pull/5042 what if index by id by @denis-yuen in https://github.com/dockstore/dockstore/pull/5052 Link MacOS instructions to GitHub action by @fhembroff in https://github.com/dockstore/dockstore/pull/5043 Fix user-level permission check for workflow version ORCID authors endpoint by @kathy-t in https://github.com/dockstore/dockstore/pull/5055 Bump actions/cache from 3.0.5 to 3.0.6 by @dependabot in https://github.com/dockstore/dockstore/pull/5067 Feature/user permissions profile page by @denis-yuen in https://github.com/dockstore/dockstore/pull/5062 deal with n/a author searching by @denis-yuen in https://github.com/dockstore/dockstore/pull/5075 Bump actions/cache from 3.0.6 to 3.0.7 by @dependabot in https://github.com/dockstore/dockstore/pull/5077 DOCK-2159: Handle duplicate keys in .dockstore.yml parse by @svonworl in https://github.com/dockstore/dockstore/pull/5074 Removing BitBucket Tokens from non-bitbucket tests by @fhembroff in https://github.com/dockstore/dockstore/pull/5076 repair dockstore-cli failing nightly build by @denis-yuen in https://github.com/dockstore/dockstore/pull/5079 allow topic update on hosted by @denis-yuen in https://github.com/dockstore/dockstore/pull/5071 Revert "repair dockstore-cli failing nightly build" by @denis-yuen in https://github.com/dockstore/dockstore/pull/5080 Bump postgresql from 42.3.3 to 42.4.1 in /bom-internal by @dependabot in https://github.com/dockstore/dockstore/pull/5064 Add a type query parameter to fetch user entries. by @coverbeck in https://github.com/dockstore/dockstore/pull/5084 Feature/fix for paths maybe by @denis-yuen in https://github.com/dockstore/dockstore/pull/5083 turn on pgp signature checks by @denis-yuen in https://github.com/dockstore/dockstore/pull/5087 SEAB-4403: Revise permissions check changes by @svonworl in https://github.com/dockstore/dockstore/pull/5082 Improved Github app handling for logs by @coverbeck in https://github.com/dockstore/dockstore/pull/5070 Missed new param in merge by @coverbeck in https://github.com/dockstore/dockstore/pull/5090 Index Elasticsearch if mappings don't exist by @kathy-t in https://github.com/dockstore/dockstore/pull/5081 optimize files get endpoint by @denis-yuen in https://github.com/dockstore/dockstore/pull/5092 Bump actions/cache from 3.0.7 to 3.0.8 by @dependabot in https://github.com/dockstore/dockstore/pull/5095 Feature/debug GitHub action by @denis-yuen in https://github.com/dockstore/dockstore/pull/5098 add git permissions check for workflows by @denis-yuen in https://github.com/dockstore/dockstore/pull/5094 SEAB-4625: Harmonize EntryVersionHelper "sourcefiles" methods by @svonworl in https://github.com/dockstore/dockstore/pull/5089 Fix multi-arch Quay images by @kathy-t in https://github.com/dockstore/dockstore/pull/5093 check whether a manual tool repo is valid by @denis-yuen in https://github.com/dockstore/dockstore/pull/5096 Sync GitHub app entry metadata with default version by @kathy-t in https://github.com/dockstore/dockstore/pull/5101 Automatically regenerate github tokens in old style on start-up by @denis-yuen in https://github.com/dockstore/dockstore/pull/5102 Add connection pool health check by @kathy-t in https://github.com/dockstore/dockstore/pull/5112 Feature/dock 2058/fix relative absolute file conversion bug by @svonworl in https://github.com/dockstore/dockstore/pull/5110 SEAB-4837: Fix sourcefile retrieval - SAM - google token bug by @svonworl in https://github.com/dockstore/dockstore/pull/5115 Fix failing workflow snapshot by @kathy-t in https://github.com/dockstore/dockstore/pull/5120 update regression test requirements by @denis-yuen in https://github.com/dockstore/dockstore/pull/5126 SEAB-4849: Fix SAM access to hosted workflows by @svonworl in https://github.com/dockstore/dockstore/pull/5127 New Contributors @fhembroff made their first contribution in https://github.com/dockstore/dockstore/pull/490