K8s: Editing vs Patching vs Updating - kubernetes

In the kubectl Cheat Sheet (https://kubernetes.io/docs/reference/kubectl/cheatsheet/), there are 3 ways to modify resources. You can either update, patch or edit.
What are the actual differences between them and when should I use each of them?

I would like to add a few things to night-gold's answer. I would say that there are no better and worse ways of modifying your resources. Everything depends on particular situation and your needs.
It's worth to emphasize the main difference between editing and patching namely the first one is an interactive method and the second one we can call batch method which unlike the first one may be easily used in scripts. Just imagine that you need to make change in dozens or even a few hundreds of different kubernetes resources/objects and it is much easier to write a simple script in which you can patch all those resources in an automated way. Opening each of them for editing wouldn't be very convenient and effective. Just a short example:
kubectl patch resource-type resource-name --type json -p '[{"op": "remove", "path": "/spec/someSection/someKey"}]'
Although at first it may look unnecessary complicated and not very convenient to use in comparison with interactive editing and manually removing specific line from specific section, in fact it is a very quick and effective method which may be easily implemented in scripts and can save you a lot of work and time when you work with many objects.
As to apply command, you can read in the documentation:
apply manages applications through files defining Kubernetes
resources. It creates and updates resources in a cluster through
running kubectl apply. This is the recommended way of managing
Kubernetes applications on production.
It also gives you possibility of modifying your running configuration by re-applying it from updated yaml manifest e.g. pulled from git repository.
If by update you mean rollout ( formerly known as rolling-update ), as you can see in documentation it has quite different function. It is mostly used for updating deployments. You don't use it for making changes in arbitrary type of resource.

I don't think I have the answer to this but I hope this will help.
All three methods do the same thing, they modify some resources configuration but the command and way to it is not the same.
As describe in the documentation:
Editing is when you open the yaml configuration file that is in the kubernetes cluster and edit it (with vim or other) to get direct modification on your cluster. I would not recommand this outside of testing purpose, reapplying conf from orignal yaml file will delete modificaitons.
Patching seems the same to me, but without opening the file and targetting specific parts of the resources.
Updating in the documentation it seems that's it's all other method to update a resource without using patch or edit. Some of those can be used for debug/testing, for example forcing a resource replace, or update an image version. Others are used to update them with new configurations.
From experience, I only used editing and some command of update for testing, most of time I reapply the configurations.

Related

How to use Kustomize and create an env like: "http://${namePrefix}service-a/some-path" or "jdbc:db2://${namePrefix}service-b:${dbPort}/${dbName}"

Lets say I need to create environment variables or ConfigMap entries like this:
- name: JDBC_URL
value: "jdbc:db2://alice-service-a:50000/db1"
- name: KEYCLOAK_BASE_URL
value: "http://alice-keycloak:8080/auth"
Where alice- is the namePrefix. How do I do this using Kustomize?
The containers I use actually do need references to other containers that are string concatenations of "variables" like above.
It doesn't look like Kustomize's vars can do this. The documentation entry Unstructured Edits seems to describe this and is under a heading called "Eschewed Features", so I guess that isn't going to happen. A similar feature request, #775 Support envsubst style variable expansion was closed.
Coming from Helm, that was easy.
What are my options if I want to move from Helm to Kustomize, but need to create an env or ConfigMap entry like e.g. jdbc:db2://${namePrefix}-service-b:${dbPort}/${dbName} (admittedly a contrived example)?
I'm guessing I'll have to resort to functionality external to Kustomize, like envsubst. Are there any best practices for cobbling this together, or am I writing my own custom-deploy-script.sh?
I'm afraid I've come up against one of the limitations of Kustomize.
The State of Kubernetes Configuration Management: An Unsolved Problem | by Jesse Suen | Argo Project has this to say under "Kustomize: The Bad":
No parameters & templates. The same property that makes kustomize applications so readable, can also make it very limiting. For example, I was recently trying to get the kustomize CLI to set an image tag for a custom resource instead of a Deployment, but was unable to. Kustomize does have a concept of “vars,” which look a lot like parameters, but somehow aren’t, and can only be used in Kustomize’s sanctioned whitelist of field paths. I feel like this is one of those times when the solution, despite making the hard things easy, ends up making the easy things hard.
Instead, I've started using gomplate: A flexible commandline tool for template rendering in addition to Kustomize to solve the challenge above, but having to use two tools that weren't designed to work together is not ideal.
EDIT: We ended up using ytt for this instead of gomplate.
I can heavily recommend the article: The State of Kubernetes Configuration Management: An Unsolved Problem. Nice to know I'm not the only one hitting this road block.

What is the practical difference between a sub-workflow and the includes directive? [Snakemake]

In the Snakemake documentation, the includes directive can incorporate all of the rules of another workflow into the main workflow and apparently can show up in snakemake --dag -n | dot -Tsvg > dag.svg. Sub-workflows, on the other hand, can be executed prior to the main workflow should you develop rules which depend on their output.
My question is: how are these two really different? Right now, I am working on a workflow, and it seems like I can get by on just using includes and putting the name of the output in rule all of the main workflow. I could probably even place the output in the input of a main-workflow rule, making the includes workflow execute prior to that rule. Additionally, I can't visualize a DAG which includes the sub-workflow, for whatever reason. What do sub-workflows offer that the includes directive can't do?
The include doesn't "incorporate another workflow". It just adds the rules from another file, like if you add them with copy/paste (with a minor difference that include doesn't affect your target rule). The subworkflow has an isolated set of rules that work together to produce the final target file of this subworkflow. So it is well structured and isolated from both main workflow and other subworkflows.
Anyway, my personal experience shows that there are some bugs in Snakemake that make using subworkflows quite difficult. Including the file is pretty straightforward and easy.
I've never used subworkflows, but here's a case where it may be more convenient to use them rather than the include directives. (In theory, I think you don't need include and subworkflow as you could write everything in a massive Snakefile, the point is more about convenience.)
Imagine you are writing a workflow that depends on result files from a published work (or from a previous project of yours). The authors did not make public the files you need but they provide a snakemake workflow to produce them. Their snakemake workflow may be quite complex and the files you need may be just intermediate steps. So instead of making sense of the all workflow and parsing it into your own include directives, you use subworkflow to generate the required file(s). E.g.:
subworkflow jones_etal:
workdir:
"./jones_etal"
snakefile:
"./jones_etal/Snakefile"
rule all:
input:
'my_results.txt',
rule one:
input:
jones_etal('from_jones.txt'),
output:
'my_results.txt',
...

Validate Kubernetes Object Creation

I would like to implement functionality (or even better reuse existing libraries/APIs!) that would intercept a kubectl command to create an object and perform some pre-creation validation tasks on it before allowing kubectl command to proceed.
e.g.
check various values in the yaml against external DB for example
check a label conforms to the internal naming convention
and so on..
Is there an accepted pattern or existing tools etc?
Any guidance appreciated
The way to do this is by creating a ValidatingAdmissionWebhook. It's not for the faint of heart and even a brief example would be an overkill as a SO answer. A few pointers to start:
https://kubernetes.io/docs/reference/access-authn-authz/admission-controllers/#validatingadmissionwebhook
https://banzaicloud.com/blog/k8s-admission-webhooks/
https://container-solutions.com/a-gentle-intro-to-validation-admission-webhooks-in-kubernetes/
I hope this helps :-)
I usually append - - dry-run to kubectl command to check and validate the YAML config

How to replace a shared file when deploying code with Capistrano?

Update: TL;DR there seems to be no built-in way to achieve this, so a custom task is an easy solution.
Capistrano provides facilities to share files and directories over all releases. This is convenient and provides even some safety on files that should not be easily changed (or must remain the same across releases), e.g. a database configuration file.
But when it comes to replace or just update one of these shared files, I end up doing it manually, directly on the target machine. I would like to improve on that, for instance by asking Capistrano to overwrite some or all shared files when deploying. A kind of --force flag with some granularity.
I am not aware of any such kind of facility, and failing so far in my search. Any pointer?
Thinking about it
One of the reason why this facility does not exist (except that I did not find it!) is that it may be harder than it looks. For example, let's assume we have a shared database configuration file, and we exclude it from version control for security reason (common practice). Current release relies on version 1 of the DB configuration. The next release requires version 2 of the DB configuration. If the deployment goes well, everything's good. It gets harder when rolling back after some error with the new release (e.g. a regression), as version 1 must then be available.
Such automation would be cool and convenient, but dangerous as well. Yet I have practical use cases at hand.
I created a template method to do this. For example, I could have a task like this:
task :create_database_yml do
on roles(:app, :db) do
within(shared_path) do
template "local/path/to/database.yml.erb",
"config/database.yml",
:mode => "600"
end
end
end
And then I have a database.yml.erb template that uses things like fetch(:database_password) to fill in appropriate values. You can use the ask method in Capistrano to prompt for these values so they are never committed.
The implementation of template can be very simple: you just need to read the file, pass it through ERB, and then use Capistrano's upload! to place the results on the server.
My version is a little more complicated than yours probably needs to be, but in case you are curious:
https://github.com/mattbrictson/capistrano-mb/blob/7600440ecd3331945d03e059368b75849857f1fb/lib/capistrano/mb/dsl.rb#L104
One approach is to use a system configuration tool like Chef or Puppet to deploy the configuration files distinctly from Capistrano.
Another approach is to create a custom task to do this: https://coderwall.com/p/wgs6gw/copy-local-files-to-remote-server-using-capistrano-3
I personally don't change on-server configs often enough or on enough servers yet to have tried to automate it. Crafting an scp command which copies the desired config file to all of the required servers has sufficed in the past.

How to handle environment-specific application configuration organization-wide?

Problem
Your organization has many separate applications, some of which interact with each other (to form "systems"). You need to deploy these applications to separate environments to facilitate staged testing (for example, DEV, QA, UAT, PROD). A given application needs to be configured slightly differently in each environment (each environment has a separate database, for example). You want this re-configuration to be handled by some sort of automated mechanism so that your release managers don't have to manually configure each application every time it is deployed to a different environment.
Desired Features
I would like to design an organization-wide configuration solution with the following properties (ideally):
Supports "one click" deployments (only the environment needs to be specified, and no manual re-configuration during/after deployment should be necessary).
There should be a single "system of record" where a shared environment-dependent property is specified (such as a database connection string that is shared by many applications).
Supports re-configuration of deployed applications (in the event that an environment-specific property needs to change), ideally without requiring a re-deployment of the application.
Allows an application to be run on the same machine, but in different environments (run a PROD instance and a DEV instance simultaneously).
Possible Solutions
I see two basic directions in which a solution could go:
Make all applications "environment aware". You would pass the environment name (DEV, QA, etc) at the command line to the app, and then the app is "smart" enough to figure out the environment-specific configuration values at run-time. The app could fetch the values from flat files deployed along with the app, or from a central configuration service.
Applications are not "smart" as they are in #1, and simply fetch configuration by property name from config files deployed with the app. The values of these properties are injected into the config files at deploy-time by the install program/script. That install script takes the environment name and fetches all relevant configuration values from a central configuration service.
Question
How would/have you achieved a configuration solution that solves these problems and supports these desired features? Am I on target with the two possible solutions? Do you have a preference between those solutions? Also, please feel free to tell me that I'm thinking about the problem all wrong. Any feedback would be greatly appreciated.
We've all run into these kinds of things, particularly in large organizations. I think it's most important to manage your own expectations first, and also ask whether it's really necessary to tell every system and subsystem on a given box to "change to DEV mode" or "change to PROD mode". My personal recommendation is as follows:
Make individual boxes responsible for a different stage - i.e. "this is a DEV box", and "this is a PROD box".
Collect as much of the configuration that differs from box to box in one location, even if it requires soft links or scripts that collect the information to then print out.
A. This way, you can easily "dump this box's configuration" in two places and see what differs, for example after a new deployment.
B. You can also make configuration changes separate from software changes, at least to some degree, which is a good way to root out bugs that happen at release time.
Then have everything base its configuration on something/somewhere that is not baked-in or hard-coded - just make sure to collect and document it in that one location. It almost doesn't matter what the mechanism is, which is a good thing, because some systems just don't want to be forced to use some mechanisms or others.
Sorry if this is too general an answer - the question was very general. I've worked in several large software-based organizations before, and this seemed to be the best approach. Using a standalone server as "one unit of deployment" is the most realistic scenario (though sometimes its expensive), since applications affect each other, and no matter how careful you are, you destabilize a whole system when you move any given gear or cog.
The alternative gets very complex very quickly. You need to start rewriting the applications that you have control over in order to have them accept a "DEV" switch, and you end up adding layers of kludge to the ones you don't have control over. Usually, the ones you don't have control over at least base their properties on something defined on a system-wide level, unless they are "calling the mothership for instructions".
It's easier to redirect people to a remote location and have them "use DEV" vs "use PROD" than it is to "make this machine run like DEV" vs "make this machine run like PROD". And if you're mixing things up, like having a DEV task run together on the same box as a PROD task, then that's not a realistic scenario anyways: I guarantee that eventually you will be granting illegal DEV-only access to somebody on PROD, and you'll have a DEV task wipe out a PROD database.
Hope this helps. Let me know if you'd like to discuss more specifics involved.
I personally prefer solution 2 (the app should know itself, by its configuration, what environment it is running in). With solution 1 (pass the environment name as a startup parameter) the danger of using the wrong environment specifier is much too high. Accessing the TEST database from PROD code and vice versa may cause mayhem, if the two installed code bases are not of the same version, as is often the case.
My current project uses solution 1, but I don't like that. A previous project I worked on used a variation of solution 2: The build process generated one setup file for every environment, making sure that they contained the same code base but appropriate configuration paramters. That worked like a charm, but I know it contradicts the paradigm that the "exact same build files must be deployed everywhere".
I think I have asked a related, self-answered, question, before I read this one : How to organize code so that we can move and update it without having to edit the location of the configuration file? . So, on that basis, I provide an answer here. I don't like the idea of "smart" application (solution 1 here) for such a simple task as finding environment settings. It seems a complicated framework for something that should be simple. The idea of an install script (solution 2 here) is powerful, but it is useful to allow the user to change the content of the config file, but would it allow to change the location of this config file? What is this "central configuration service", where is it located? My answer is that I would go with option 2, if the goal is to set the content of the configuration file, but I feel that the issue of the location of this configuration file remains unanswered here.
If you're using JSON to store/transmit configuration (or can use JSON in your pre-deploy process to output to some other format) you can annotate key/property names for environment/context-specific values with arbitrary or environment-specific suffixes, and then dynamically prefer/discriminate them at build/deploy/run/render -time, while leaving un-annotated properties alone.
We have used this to avoid duplicating entire configuration files (with the associated problems well known) AND to reduce repetition. The technique is also perfect for internationalization (i18n) -- even within the same file, if desired.
Example, snippet of pre-processed JSON config:
var config = {
'ver': '1.0',
'help': {
'BLURB': 'This pre-production environment is not supported. Contact Development Team with questions.',
'PHONE': '808-867-5309',
'EMAIL': 'coder.jen#lostnumber.com'
},
'help#www.productionwebsite.com': {
'BLURB': 'Please contact Customer Service Center',
'BLURB#fr': 'S\'il vous plaît communiquer avec notre Centre de service à la clientèle',
'BLURB#de': 'Bitte kontaktieren Sie unseren Kundendienst!!1!',
'PHONE': '1-800-CUS-TOMR',
'EMAIL': 'customer.service#productionwebsite.com'
},
}
... and post-processed (in this case, at render time) given dynamic, browser-environment-known location.hostname='www.productionwebsite.com' and navigator.language of 'de'):
prefer(config,['www.productionwebsite.com','de']); // prefer(obj,string|Array<string>)
JSON.stringify(config); // {
'ver': '1.0',
'help': {
'BLURB': 'Bitte kontaktieren Sie unseren Kundendienst!!1!',
'PHONE': '1-800-CUS-TOMR',
'EMAIL': 'customer.service#productionwebsite.com'
}
}
If a non-annotated ('base') property has no competing annotated property, it is left alone (presumably global across environments) otherwise its value is replaced by an annotated value, if the suffix matches one of the inputs to the preference/discrimination function. Annotated properties that do not match are dropped entirely.
You can mix and match this behaviour to annotate configuration to achieve distinctions of global, default, specific that are (assuming you're sensible) readable with zero/minimal duplication.
The single, recursive prefer() function (as we're calling it, lacking the need or desire to make an entire project/framework out of it) we've developed so far (see jsFiddle, with inline docs) goes a bit further than this simple example, and (explained in greater detail here) handles deeply-nested configuration objects, as well as preferential ordering and (if you need to stay flat) combination of suffixes.
The function relies on JS ability to reference object properties as strings, dynamically, and tolerate # and & delimiters in property names which are not valid in dot-notation syntax but consequently (help) prevent developers from breaking this technique by accidentally referring to pre-processed/annotated attributes in code (unless they, non-conventionally don't prefer to use dot-notation.)
We have yet to have this break anything for us, nor have we been schooled on any fundamental flaws of this technique, beyond irresponsible/unintended usage or investment/fondness for existing frameworks/techniques that pre-exist. We have also not profiled it for performance (we only tend to run this once per build/session, etc.) so in your own usage, YMMV.
Most configurations transmitted client-side of course would not want to contain sensitive pre-production values, so one could (should!) use the same function to generate a production-only version (with no annotations) in pre-deploy, while still enjoying a SINGLE configuration file upstream in your process.
Further, if you're doing this for i18n, you may not want the entire wad going over the wire, so could process it server-side (cached or live, etc.) or pre-process it in build/deploy by splitting into separate files, but STILL enjoying a single source of truth as early in your workflow as possible.
We have not explored implementing the same function in Java (or C#, PERL, etc.) assuming it's even possible (with some exotic reflection maybe?) but a build environment that includes NodeJS could farm that step out easily.
Well if it suits your needs and you have no problem of storing the connection strings in the source control repository, you could create files like:
appsettings.dev.json
appsettings.qa.json
appsettings.staging.json
And choose the right one in the deployment script and rename it to the actual appsettings.json, which is then read by your app.