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chore: merge repositories into new branch (main) #163
Commits on Jun 21, 2018
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Commits on Jun 26, 2018
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maintenance: Use python's standard formatting
autopep8 was used for applying the formatting, a few manual changes were made to make some changes more pallatable
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Commits on Jun 27, 2018
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Commits on Jun 28, 2018
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Commits on Jun 29, 2018
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Commits on Sep 17, 2018
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fixes: closing files & conns; regex bugs
Now files and connections are more consistently closed. Most regular expressions produced bugs and have been replaced. Transput class now contains all the virtual functions that are to be inherited. Logging messages are lazy-loaded now. Uploading HTTP folders now tries to upload all the files, not just the last one found. Renamed some variables to make their purpose more obvious Stop raising exceptions for the time being as the rest of the code does not handle them, return the error code instead
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maintenance: less biolerplate to close connections
Use transputs as context managers to be less verbose for closing connections
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maintenance: use enums instead of strings
This way the code won't fail in subtle ways
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Commits on Sep 18, 2018
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Commits on Sep 19, 2018
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Commits on Oct 2, 2018
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Commits on Oct 30, 2018
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Commits on Jan 21, 2019
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According to Ania, this is the old version that is not used anymore.
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Commits on Jan 22, 2019
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Commits on Jan 23, 2019
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[#12] FileTransput.download_file()
TODO It's still using the host path. This has to be translated to a path inside the container.
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Commits on Jan 24, 2019
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Commits on Jan 25, 2019
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[#12] ren transput_filer.py => filer.py (continued...)
I forgot to rename in one of the tests.
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Commits on Jan 28, 2019
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- moved to scripts/ - it was always executing 'taskmaster' (hard-coded)
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dockerRun: forwarding cmd line args to the image.
Before, they were simply discarded.
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Commits on Jan 29, 2019
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Commits on Feb 1, 2019
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[#12] install: no longer creating links
Why? Because that way, './taskmaster' wouldn't run the current code: it would run _the last installed code_ ('pip install .'). I.e. one more thing for you to remember. If you forgot about this, it could easily lead to hours of head scratching and fruitless debugging.
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Commits on Feb 4, 2019
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[#12] Adding mount to CONTAINER_BASE_PATH ('/transfer')
* test_mounts * test_run_task
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Commits on Feb 5, 2019
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[#12] /transfer mount: minor errors in the spec
* 'hostPath' : { 'path' : '/transferAtNode' } * .append() => .extend()
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run: deleting everything before + examples/
(everything = pods + jobs + pvc)
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Commits on Feb 6, 2019
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Commits on Feb 8, 2019
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Commits on Feb 11, 2019
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[#12] upload/download methods: refactoring (transfer())
def download_file(self): self.transfer(shutil.copy , self.urlContainerPath , self.path) def upload_dir(self): self.transfer(shutil.copytree , self.path , self.urlContainerPath)
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[#12] 'file:' protocol disabled if any of (HOST_BASE_PATH, CONTAINER_…
…BASE_PATH) is undefined.
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[#12] transfer mount: making it optional
The relevant conf is added to filer spec only if both (HOST_BASE_PATH, CONTAINER_BASE_PATH) are defined.
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Commits on Feb 12, 2019
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Limitation of shutil.copytree: > The destination directory, named by dst, must not already exist; it will be created as well as missing parent directories.
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Commits on Feb 15, 2019
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Commits on Feb 20, 2019
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Commits on Feb 21, 2019
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[#12] Fix: TRANSFER_VOLUME_NAME => TRANSFER_PVC_NAME
I parameterized the wrong constant. It should have been 'transfer-pvc' -- not 'transfer-volume'.
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Commits on Feb 22, 2019
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[#12] --pull-policy-always: binding cmd line arg => what ends up in F…
…iler() Plus: changed Filer() param from string => boolean.
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Commits on Oct 18, 2019
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Dropping Python 2 support from the project: - setup.py no longer advertises Python 2 in supported interpreters - tox.ini does not use py27 environment - renamed some unit tests to be automatically picked up by pytest - pytest is meant to be used through tox (not from setup.py) for unit tests - removed unnecessary Python 2 dependencies (future, unittest2, enum34) - bumped up kubernetes to 6.1.0 because of syntax error when using 5.0.0 in Python 3.7 - using entry points instead of script names (renamed filer.py to filer)
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Building Docker images with Python 3.7
- changed the base image to Alpine 3.10 with Python 3.7. - two staged build: (1) build wheel (2) install wheel and its dependencies - system-dependent Python directory layout knowlegde is no longer needed - docker will now ignore expensive .tox and other build directories while building images - image entrypoints edited to match "filer" and "taskmaster" installed binaries
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Commits on Oct 21, 2019
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Commits on Oct 27, 2019
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Docker WORKDIR fixes, CI improvements
- Removed WORKDIR from Dockerfiles - Python 3.7 added to Travis - Added extra Pylint step to fail on errors (E) only
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Commits on Apr 16, 2020
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Commits on May 18, 2020
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Merge pull request #4 from EMBL-EBI-TSI/elixir-groups
Elixir groups
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Commits on May 19, 2020
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Commits on May 27, 2020
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Commits on Jun 3, 2020
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Merge pull request #5 from EMBL-EBI-TSI/extra-secrets
Global secrets for executors
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Commits on Jun 16, 2020
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Allow changing the default filer image name using TESK_API_TASKMASTER…
…_FILER_IMAGE_NAME environment variable
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Merge pull request #14 from Zcowyzrg/py27remove
Remove Python 2 support
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Commits on Jun 17, 2020
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Merge pull request #17 from EMBL-EBI-TSI/extra-secrets
Allow volumes (e.g. secrets) in the executor spec
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Commits on Jun 22, 2020
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Commits on Jun 23, 2020
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Merge pull request #16 from lvarin/filer_image_name
Allow changing the default filer image name using -fn
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Commits on Jun 30, 2020
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Now a different function is used in the code. Also a couple of tests were added to increase coverage
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Commits on Jul 6, 2020
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fix(ftp): stopped ftp errors silencing
FTP errors were not propagated, resulting in jobs completing while FTP errors were present (#20)
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Commits on Jul 7, 2020
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feat(api): variable jobs backoff limits
By defining new environment variables, TESK_API_FILER_ENVIRONMENT_BACKOFF_LIMIT and TESK_API_EXECUTOR_ENVIRONMENT_BACKOFF_LIMIT, the number of a retires before a job fails can be explicitly set
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Commits on Jul 8, 2020
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Commits on Jul 9, 2020
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Add support to netrc in filer.py.
If the environment variable 'NETRC_SECRET_NAME' is present, and the content of the secret is a valid netrc file, it will be used for authentication.
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Commits on Jul 13, 2020
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Commits on Jul 14, 2020
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Commits on Jul 15, 2020
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Commits on Jul 17, 2020
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Merge pull request #25 from EMBL-EBI-TSI/localfile-regression
Fix local filesystem regression of error checking
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Commits on Jul 21, 2020
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Quick and dirty fix, took a while to find the spot, buit it fixes the…
… scientific notation bug and the too small memory bug
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Commits on Jul 29, 2020
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Merge branch 'variable-backoff-limit' of git://github.com/stikos/tesk…
…-core into stikos-variable-backoff-limit
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Clarify passthrough of env vars
TESK API passes variables with a specific prefix to taskmaster, but the prefix is stripped.
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Commits on Jul 31, 2020
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Commits on Aug 5, 2020
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Merge pull request #26 from cibinsb/testing_taskmaster
More unittesting
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Commits on Aug 6, 2020
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Commits on Aug 12, 2020
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fix for s3 credentials through secret
Tested and working. Secret name is hardcoded.
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Since the 'endpoint_url' parameter inside the aws config file is not handled by boto, we need a simple utility module to extract it.
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Commits on Aug 18, 2020
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Merge pull request #9 from lvarin/fix_memory
Quick and dirty fix to scientific notation problem and 0 ram requirements (support for Nextflow, but worth having anyway, until we bump K8s client version)
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Commits on Aug 25, 2020
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Some simple unit tests test additions additional tests (pytest) Created more tests for ftp filer operations with pytest in a separate file additional tests for ftp, http removed print statement updated setup.py test dependencies enable Travis filer unit tests improvements Files are no longer created during tests, enhanced testing for ftp_download tests fixes removed file exists test Removed f-strings for python3.5 compliance http upload dir test add fs fixture correct fixture name added fs in test deps ignore calls order test for ftp upload dir add pytest config mock ftplib connect added ftp download dir test removed ftpserver.stop and redundant login, connect removed unnecessary dependencies filer tests enhancements tests adjustments for rebase file creation assertion & commented code removal assert mock_open called_with() fixed duplicate code issue
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feat: dynamic storage provisioning
The storage class used is now configurable through the use of the TESK_API_TASKMASTER_ENVIRONMENT_STORAGE_CLASS_NAME environment variable. If no value is provided, the default storage class will be used. (#111)
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And we will move HOME for .netrc to fix #31
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Bump urllib3 from 1.22 to 1.24.2
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.22 to 1.24.2. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/master/CHANGES.rst) - [Commits](urllib3/urllib3@1.22...1.24.2) Signed-off-by: dependabot[bot] <[email protected]>
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Merge pull request #29 from stikos/s3-creds-test
Support S3 credentials configuration through secrets
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Allow unit tests to run under python3.8
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Remove Python3.5 support from unit tests
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Add Python3.8 to travis testing and remove 3.5
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Merge pull request #36 from justincc/run-unit-tests-with-python3.8
Allow unit tests to run under python3.8
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Merge pull request #35 from cibinsb/storage_class_error
Bug Fix: When polling pod.status.start_time.
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adding testcases and condition to check particular exceptions
Cibin Sadasivan Baby committedDec 3, 2020 Configuration menu - View commit details
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Cibin Sadasivan Baby committed
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Merge pull request #37 from cibinsb/improving_Taskmaster
Enabling taskmaster process run more than once (for instance in case of transient error). It should resume execution where it finished, based on state of objects (pvc, filers and executors) in K8s API.
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Merge pull request #17 from EMBL-EBI-TSI/tes-1
TES 1.0 compatibility
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Merge pull request #20 from EMBL-EBI-TSI/package-rearrange
Package rearrange
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Bump urllib3 from 1.24.2 to 1.26.5
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.24.2 to 1.26.5. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@1.24.2...1.26.5) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
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Upgrade io.kubernetes library to v11.0.1. Changes needed:
- Model objects where moved to a different package - Memory and CPU request is defined using Quantity and not String - Some functions got more (optional) parameters
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Upgrade com.google.guava to v30.0-jre due to moderate severity securi…
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Merge pull request #28 from lvarin/guava-30.0-jre
Upgrade com.google.guava to v30.0-jre
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Merge pull request #38 from elixir-cloud-aai/dependabot/pip/urllib3-1…
….26.5 Bump urllib3 from 1.24.2 to 1.26.5
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Merge pull request #33 from stikos/111-configurable-pvc
feat: customizable storage class
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Milan committed
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Add user 100 to filer and taskmaster
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Merge pull request #25 from elixir-cloud-aai/dependabot/maven/io.kube…
…rnetes-client-java-11.0.1 Bump client-java from 1.0.0-beta1 to 11.0.1
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Switch to GitHub Actions instead of Travis CI (#33)
* Added workflow files * Added code coverage to checks * Added synchronize event for PRs
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Merge pull request #26 from lvarin/LimitRange-query
Limit range query
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Add two properties to the file 'application.properties' so the new ve…
…rsions are configured properly
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* Fix space * Add more and better caches to exceptions * Convert value with only 6 decimals * Remove untested catch clauses * Remove untested catch clauses * Remove untested catch clauses
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ci: add publish Docker workflow (#45)
Co-authored-by: Milan <[email protected]>
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Merge pull request #40 from elixir-cloud-aai/testing-gh-action
ci: add GitHub Actions workflows
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Co-authored-by: Martin Kuba <[email protected]>
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Co-authored-by: Martin Kuba <[email protected]>
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Merge pull request #29 from lvarin/upgrade-org.springframework.boot-2…
….6.1 Upgrade to org.springframework.boot to v2.6.1
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Add securityContext settings (#46)
* Add securityContext settings * Fix tests
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* Use configmap for JSON_INPUT Signed-off-by: Lukas Hejtmanek <[email protected]> * Fix basic tests Signed-off-by: Lukas Hejtmanek <[email protected]> * Fix integration tests Signed-off-by: Lukas Hejtmanek <[email protected]> Signed-off-by: Lukas Hejtmanek <[email protected]>
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fix: api-docs JSON example (#30)
* Add junit deps * Fix api-docs JSON example The api-docs json definition of the API was not passing the JSON parsing. One of the examples (in colunm ~1580, with text us-west-1), needed quotes * Upgrade springfox-swagger to fix swagger API deffinition * Few other changes to make it more compatible * Fix missing dependencies
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Bump urllib3 from 1.26.5 to 1.26.18
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.5 to 1.26.18. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@1.26.5...1.26.18) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
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* Downgrade springfox-swagger.version for tests. Do not use this * Followed https://github.com/springfox/springfox\#migrating-from-earlier-snapshot * Added Guava back
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Update gha, docker login (#54)
Co-authored-by: Tristan <[email protected]>
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Bump guava from 30.0-jre to 32.0.0-jre (#50)
Bumps [guava](https://github.com/google/guava) from 30.0-jre to 32.0.0-jre. - [Release notes](https://github.com/google/guava/releases) - [Commits](https://github.com/google/guava/commits) --- updated-dependencies: - dependency-name: com.google.guava:guava dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Merge pull request #46 from elixir-cloud-aai/regexp-improve
Improve S3 URL support and others
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Merge pull request #43 from elixir-cloud-aai/dependabot/pip/urllib3-1…
….26.18 Bump urllib3 from 1.26.5 to 1.26.18
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Merge pull request #47 from elixir-cloud-aai/improve-local-build
Make a bit better the scripts
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Merge remote-tracking branch 'tesk-core/master'
# Conflicts: # .gitignore # .travis.yml # LICENSE # MANIFEST.in # README.md # charts/tesk/templates/openshift/oc-route.yaml # cloudbuild.yaml # cloudbuild_testing.yaml # documentation/img/TESKlogo.png # documentation/img/TESKlogowfont.png # setup.py
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* Chart and doc updates - Add securityContext. Remove of Ingress deployment in values.yaml - Update Ingress rules apiVersion - Update README and deployment documentation - Update condition for OpenShift Route * Enable ingress.rules * Add limits & requests
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Fix links to deployment.md (previously deployment_new.md) (#147)
* WIP: Update GitHub Actions workflow * Fix links to deployment.md (previously deployment_new.md)
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