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Update/latest #4

Merged
merged 73 commits into from
Jan 25, 2024
Merged

Update/latest #4

merged 73 commits into from
Jan 25, 2024

Commits on Mar 3, 2023

  1. Adding the ability to deploy a seperate postgres instance for each se… 

    …rvice
    @EliseCastle23
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  2. setting the default to 'false' for creating a separate postgres insta… 

    …nce for each service
    @EliseCastle23
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Commits on Mar 8, 2023

  1. Fixing lint issues

    @EliseCastle23
    EliseCastle23 committed Mar 8, 2023
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  2. removing the indent to resolve linting issues

    @EliseCastle23
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  3. forgot to make the same changes to wts and sheepdog

    @EliseCastle23
    EliseCastle23 committed Mar 8, 2023
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  4. Merge pull request uc-cdis#103 from uc-cdis/feat/GPE-796 

    GPE-796 Adding the ability to deploy a separate Postgres instance for each service.
    @EliseCastle23
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Commits on Mar 13, 2023

  1. Add small fixes, pin peregrine to 2023.01, portal to master (uc-cdis#104 

    )

* Add small fixes, pin peregrine to 2023.01, portal to master
    @jawadqur
    jawadqur authored Mar 13, 2023
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  2. Adding/modifying some of the documentation for the values of the subc… 

    …harts.

Moves liveness probe, readiness probe, and ports from values.yaml to deployment.yaml where applicable.

Removed Datadog environment variables in 3 subcharts as they are not being used atm.
    @EliseCastle23
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  3. Merge branch 'master' into feat/GPE-623

    @EliseCastle23
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  4. correcting the chart versions

    @EliseCastle23
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Commits on Mar 14, 2023

  1. correcting the dependency chart version

    @EliseCastle23
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  2. removing trailing spaces to get rid of linting errors

    @EliseCastle23
    EliseCastle23 committed Mar 14, 2023
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  3. removing trailing spaces from audit

    @EliseCastle23
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  4. missed some trailing spaces

    @EliseCastle23
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  5. missed some trailing spaces

    @EliseCastle23
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  6. bumping up elasticsearch version to see if linting issue will resolve

    @EliseCastle23
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Commits on Mar 15, 2023

  1. removing more trailing spaces

    @EliseCastle23
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  2. Merge pull request uc-cdis#105 from uc-cdis/feat/GPE-623 

    Adding/modifying some of the documentation for the values of the subc…
    @EliseCastle23
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  3. Fix sheepdog configuration (uc-cdis#107)

    @jawadqur
    jawadqur authored Mar 15, 2023
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Commits on Mar 16, 2023

  1. Fix error in manifestservice yaml (uc-cdis#108) 

    * Fix error in manifestservice
    @jawadqur
    jawadqur authored Mar 16, 2023
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  2. correcting selector label mismatch for the manifestservice (uc-cdis#109) 

    * correcting selector label mismatch for the manifestservice

* bumping up the chart version
    @EliseCastle23
    EliseCastle23 authored Mar 16, 2023
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Commits on Mar 30, 2023

  1. Adding a new labeling strategy for our Helm charts (uc-cdis#110) 

    * Adding a new labeling strategy for our Helm charts- starting with Arborist.

Will also conditionally include Datadog environment variables.

* bumping up the chart version and making variables for the datadog_setup.tpl

* fixing linting issues

* adding code reusability for labeling and datadog labels/environment variables. Made each chart have consistent labeling.

* updating the dependency chart versions for umbrella chart

* fixing the labeling for indexd and manifest service, so we don't produce an error on install

* fix for linting errors

* resolving blank line error for linting

* Add uwsgi.ini override for indexd

---------

Co-authored-by: Jawad Qureshi <[email protected]>
    @EliseCastle23 @jawadqur
    EliseCastle23 and jawadqur authored Mar 30, 2023
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Commits on Apr 7, 2023

  1. Fix bug in indexd and presigned-url-fence (uc-cdis#114)

    @jawadqur
    jawadqur authored Apr 7, 2023
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Commits on Apr 13, 2023

  1. Add CONTRIBUTION.md (uc-cdis#115) 

    * Add CONTRIBUTION.md

* Docs/contributor review (uc-cdis#112)

* Updates to contributing.md

* Update Contributing.md

* Move the CONTRIBUTING.md file to root

* Adding issues and communication channels (uc-cdis#117)

* Update CONTRIBUTING.md

* remove DS_store

* Delete .gitignore

* Create .gitignore

* Update .gitignore

* Update .gitignore

* Update CONTRIBUTING.md

* add .DS_Store to .gitignore

---------

Co-authored-by: michaelfitzo <[email protected]>
    @jawadqur @michaelfitzo
    jawadqur and michaelfitzo authored Apr 13, 2023
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Commits on May 4, 2023

  1. adding pod disruption budgets to help improve availability. The commo… 

    …n chart has the pdb template and each chart has the ability to enable the pdb from the global values section. The gen3 umbrella chart also has this ability and will override the subchart options if enabled.
    @EliseCastle23
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  2. updated the commons chart version.

    @EliseCastle23
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  3. bumping up elasticsearch chart version

    @EliseCastle23
    EliseCastle23 committed May 4, 2023
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  4. Merge pull request uc-cdis#122 from uc-cdis/feat/GPE-946 

    adding pod disruption budgets to help improve availability. The commo…
    @EliseCastle23
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Commits on May 8, 2023

  1. Documentation and various fixes/updates (uc-cdis#121) 

    - Add sower helm chart
- Add more documentation 
- Add custom ingress resource
    @jawadqur
    jawadqur authored May 8, 2023
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  2. Remove unused global bucket configuration (uc-cdis#127)

    @jawadqur
    jawadqur authored May 8, 2023
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Commits on May 12, 2023

  1. Setting up usersync job for helm. 

    Adding documentation on how to setup the job.

Updating all relevant charts global config options.
    @EliseCastle23
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  2. testing a fix for linting error.

    @EliseCastle23
    EliseCastle23 committed May 12, 2023
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  3. fixing chart.yaml for gen3 umbrella chart

    @EliseCastle23
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Commits on May 15, 2023

  1. forgot to bump up the common chart version.

    @EliseCastle23
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  2. updating the gen3 umbrella chart

    @EliseCastle23
    EliseCastle23 committed May 15, 2023
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  3. fixing indentation and trailing spaces in fence values.yaml file

    @EliseCastle23
    EliseCastle23 committed May 15, 2023
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  4. moving the seperator in the serviceaccount.yaml file

    @EliseCastle23
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  5. changing separator location

    @EliseCastle23
    EliseCastle23 committed May 15, 2023
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  6. adding an extra space

    @EliseCastle23
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  7. changin seperator again

    @EliseCastle23
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  8. adding two seperators for linting

    @EliseCastle23
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  9. moving the userync sa and cluster role to a separate sheet due to lin… 

    …ter failure.

Also, setting the default for the usersync job to "false"
    @EliseCastle23
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Commits on May 16, 2023

  1. - removing userysnc values from the global manifest and putting them … 

    …in a separate section for Fence only.

- removing configuration and references to the Fence ssh keys, config, and proxy_user as we are moving away from using squid.
    @EliseCastle23
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Commits on May 17, 2023

  1. Update workflow to use GITHUB_OUTPUT (uc-cdis#130)

    @SpencerAxelrod
    SpencerAxelrod authored May 17, 2023
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Commits on May 18, 2023

  1. commenting out the creation of the fence configmap in the usersync cr… 

    …onjob for now.
    @EliseCastle23
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  2. adding "slackWebHook" environment var to init container.

    @EliseCastle23
    EliseCastle23 committed May 18, 2023
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  3. Merge branch 'master' into feat/GPE--930

    @jawadqur
    jawadqur authored May 18, 2023
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  4. Merge pull request uc-cdis#129 from uc-cdis/feat/GPE--930 

    Setting up usersync job for helm.
    @EliseCastle23
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Commits on Jun 5, 2023

  1. removing fence-ssh.yaml as it is not needed. (uc-cdis#131) 

    * removing fence-ssh.yaml as it is not needed.

* bumping up versions
    @EliseCastle23
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  2. Remove erroneous fence config (uc-cdis#132)

    @jawadqur
    jawadqur authored Jun 5, 2023
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  3. Bump gen3 chart

    @jawadqur
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  4. Merge pull request uc-cdis#133 from uc-cdis/fix/fence-ssh-error 

    Bump gen3 chart version.
    @jawadqur
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Commits on Jun 13, 2023

  1. Remove erroneous usersync configmap

    @jawadqur
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  2. Merge pull request uc-cdis#134 from uc-cdis/feat/usersync-cm-error 

    Remove erroneous usersync configmap
    @jawadqur
    jawadqur authored Jun 13, 2023
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Commits on Jul 3, 2023

  1. allowing the "imagePullPolicy" to be configurable for these charts.

    @EliseCastle23
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  2. bumping up the gen3 helm chart version

    @EliseCastle23
    EliseCastle23 committed Jul 3, 2023
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  3. correcting chart version

    @EliseCastle23
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  4. fixing chart version for sheepdog

    @EliseCastle23
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  5. Merge pull request uc-cdis#135 from uc-cdis/feat/imagePullPolicy 

    allowing the "imagePullPolicy" to be configurable for these charts.
    @EliseCastle23
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Commits on Jul 27, 2023

  1. Add role binding for sower

    @jawadqur
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Commits on Jul 31, 2023

  1. Move sower config to values

    @jawadqur
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Commits on Aug 2, 2023

  1. Merge pull request uc-cdis#137 from uc-cdis/fix/sower-rb 

    Updates to sower
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    jawadqur authored Aug 2, 2023
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Commits on Sep 21, 2023

  1. Update fence-service-ga4gh.conf

    @jawadqur
    jawadqur authored Sep 21, 2023
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  2. Update Chart.yaml

    @jawadqur
    jawadqur authored Sep 21, 2023
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  3. Update revproxy and create a new gen3 release

    @jawadqur
    jawadqur authored Sep 21, 2023
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  4. Merge pull request uc-cdis#139 from uc-cdis/jawadqur-patch-1 

    Fix erronous path in revproxy
    @jawadqur
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Commits on Oct 26, 2023

  1. added documentation to raise vm.max_map_count

    @uwwint
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  2. Merge pull request uc-cdis#145 from AustralianBioCommons/fix/document… 

    …_max_map

added documentation to raise vm.max_map_count
    @jawadqur
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Commits on Oct 27, 2023

  1. Updated pre-built portal documenation

    @flashguerdon
    flashguerdon committed Oct 27, 2023
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  2. Merge pull request uc-cdis#146 from AustralianBioCommons/fix/document… 

    …_portal_prebuilt

Updated pre-built portal documentation
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Commits on Nov 28, 2023

  1. Elasticsearch 7 support (uc-cdis#143) 

    * Initial ES7 and ETL integration

* Update gitops.json

* Add test-connection pods

* Add test-connection pods

* Add chart install + test

* Add chart install + test

* Add chart install + test

* Add chart install + test

* Add chart install + test

* Add agg-mds sync job

* Bump versions

* Update gh actions

* Update gh actions

* Fix linting issues

* Update KIND doc

* Update KIND doc

* Update ETL and ES values

* Delete local ES chart and update ETL job

* move aggMDS to cron that can be triggered
    @jawadqur
    jawadqur authored Nov 28, 2023
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Commits on Jan 24, 2024

  1. merge latest helm chart updates

    @hadams95
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  2. remove gitops json value from portal values since we that is now a mo… 

    …unted file. remove ingress_dev if we have our non-dev ingress enabled. nest gitops config under portal
    @hadams95
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