Bump io.springfox:springfox-swagger-ui from 2.7.0 to 2.10.0 #12
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Configurable reference genome in Genome Nexus VEP
Development of Better Performing Vep Wrapper * performance improvements - add computeOrder() function : computes forward and backwards remapping of order - apply forward re-ordering (to establish chromosome position order) - backwards re-ordering (to re-establish the query order) not yet applied - add extra logging for testing * Changed dataflow to send/receive file from vep * output from vep command line tool now streamed to web response (rather than file output) * input to vep command line too now provided as a file rather than stdin streaming (performance boost) * fixed plugin manager bug / maven configuration * created 2 threads to transfer the stderr and stdout streams * created a filter output stream to optionally "jsonify" the one object per line format from vep * incomplete work - fix stream transfer thread fails * add wepAPI argument for responseTimeout ( 0 indicates there is no timeout limit ) * Added logic to destroy vep process at timelimit * add complete line output buffer stream (so that records in the response are never partial) - CompleteLineBufferedOutputStream receives characters from the java Process output and bundles them into lines - LinesToJSONListFilterOutputStream receives lines and formats them into a json list .. adding commas and brackets as appropriate Co-authored-by: Angelica Ochoa <[email protected]> Co-authored-by: Avery Wang <[email protected]> Co-authored-by: Manda Wilson <[email protected]> Co-authored-by: Robert Sheridan <[email protected]>
Add xref_refseq Flag for CLT
- SystemProcessManager class now provides process management services for VEP
- uses UNIXProcess (if available) for determining a Process pid
- uses UNIXProcess (if available) for reaping zombies (via waitForProcessExit())
- determines availability of ps and kill commands on local system
- manages processes launched if needed tools are available
- starts ReaperDaemonThread when first VEP process is launched
- reaper will periodically check for orphaned child processes of a destroyed VEP process and kill them
- reaper will periodically check for zombie processes and reap them
- unix 'ps' command output parsing encapsulated in ProcessSurveyor class
- remove thread interruption in VepRunner - now StreamTransferrer threads will exit naturally when orphaned children are killed
- shut down reaper as application shuts down
Co-authored-by: Manda Wilson <[email protected]>
Co-authored-by: Robert Sheridan <[email protected]>
Previous version hanged on a dependency
Upgrade maven version
Add GitHub Action to publish docker image
Bumps [io.springfox:springfox-swagger-ui](https://github.com/springfox/springfox) from 2.7.0 to 2.10.0. - [Release notes](https://github.com/springfox/springfox/releases) - [Changelog](https://github.com/springfox/springfox/blob/master/docs/release-notes.md) - [Commits](springfox/springfox@2.7.0...2.10.0) --- updated-dependencies: - dependency-name: io.springfox:springfox-swagger-ui dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
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Bumps io.springfox:springfox-swagger-ui from 2.7.0 to 2.10.0.
Release notes
Sourced from io.springfox:springfox-swagger-ui's releases.
... (truncated)
Changelog
Sourced from io.springfox:springfox-swagger-ui's changelog.
... (truncated)
Commits
2026ff1Changed the command to include all as gradle properties87a402fFixed javadoc error. This is already fixed in openapi branch02805e1Updated java version31e90faChanging version prior to release93e4352Added release script to the repositoryc651680Merge pull request #3307 from springfox/bugfix/model-enhancement16e8941Returning cache to life.e136026Merge pull request #3304 from springfox/bugfix/model-enhancement500ddcf#33034c181b6Merge branch 'bugfix/model-enhancement'Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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