Helpers that integrate gen3 gitops configuration with kubernetes.
Apply manifest variable substitions on the given yaml file.
`gen3 gitops filter path/to/file.yaml [optional path to manifest.json] [optional key1 value1 key2 value2 ...]
Ex:
gen3 gitops filter cloud-automation/kube/services/fence/fence-deploy.yaml GEN3_DEBUG_FLAG True
Assemble the list of keys that gen3 gitops configmaps will harvest from the union of the manfiests/ subfolders, manfifest.json, manifestDefaults/ subfolders, and etl-mapping.
Update the manifest.json, manifests/ folder, and '$GEN3_HOME/gen3/lib/manifestDefaults/ derived (manifest-*) configmaps. Optionally take a list of keys to limit which configmaps to sync (subset of gen3 gitops configmaps-list` - see below).
gen3 gitops configmaps guppy
gen3 gitops configmaps etl-mapping
gen3 gitops configmaps
The configmaps command also harvests configmaps from the manifests/ subdirectory, ${GEN3_HOME}/gen3/lib/manifestDefaults/, and it also handles the etl-mapping as a one-off. For example:
cd $(dirname $(g3k_manifest_path))
mkdir -p manifests/hatchery
jq -r .hatchery < manifest.json | tee manifests/hatchery/hatchery.json
Given a folder manifests/key/ with files a.json and b.json and key.json - gitops manifests will create a configmap manifest-key with keys a.json, b.json and key.json; and it will also create a key json with the same content as key.json (to make it easy to pull values out of the root manifest.json).
Finally - the harvest also loads configuration from ${GEN3_HOME}/gen3/lib/manifestDefaults/ if that folder contains a key that does not already exist in manifest.json or the manfiests/ folder.
Note: if a key exists both under the manifests/ folder and in manifest.json, then only the data in manifests/ persists in the configmap
Note: also as a random help updates the etl-mapping configmap from etlMapping.yaml
Create a manifest- configmap from the given json blob.
gen3 gitops configmaps-from-json manifest-guppy "$guppyConfig"
Force the local cdis-manifest/ and cloud-automation/ folders to sync with github.
gen3 gitops enforce
Extract the project to resource mapping required by the etl from a user.yaml file:
gen3 gitops etl-convert < user.yaml
Get the active manifest folder path.
folder="$(gen3 gitops folder)"
Show the git history of changes to the manifest folder
gen3 gitops history
Get the path to the active manifest
path="$(gen3 gitops manifest)"
Run gen3 gitops sync on the given ssh target.
See gen3 gitops sshlist and gen3 gitops sync below.
gen3 gitops rsync [email protected]
List the cdis gen3 admin machines.
gen3 gitops sshlist
Update the dictionary URL and image versions. The --dryrun flag can be used to display dictionary URL and image version check logs but do not want to roll pods.
The optional --slack flag sends an update to the commons' slack channel (if any).
gen3 gitops sync --slack
gen3 --dryrun gitops sync
List the Gen3 source code repos.
gen3 gitops repolist
Derive the path to the -deploy.yaml for a service name
(or service-canary), and an optional deployment version -
pulled from the manifest if not given as an argument
gen3 gitops rollpath fence
gen3 gitops rollpath arborist 2
List the 5 largest semver tags associated with each Gen3 code repository.
gen3 gitops taglist
Generate the next patch release tag for the specified repository, and push to github
using the caller's ssh key for authentication.
We expect a user will usually run this command from his personal laptop which hosts her git authentication keys.
gen3 gitops dotag fence
Runs terraform to check on an environment. It'll just get the plan, it won't apply it. It must be ran as the user that manages the commons. It takes a module as argument, like: vpc, eks.
gen3 gitops tfplan vpc
Runs a terraform plan on an environment. It must be ran as the user that manages the commons. Execute this with extream precaution, it won't prompt for confirmation, will just apply. It takes a module as argument, like: vpc, eks.
gen3 gitops tfapply eks
Checks and updates the image for specific fence-related cronjobs (fence-delete-expired-clients and fence-cleanup-expired-ga4gh-info), if they do not match the image specified in the manifest-versions ConfigMap.
gen3 gitops update-fence-cronjobs